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- PDB-5yoy: Crystal structure of the human tumor necrosis factor in complex w... -

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基本情報

登録情報
データベース: PDB / ID: 5yoy
タイトルCrystal structure of the human tumor necrosis factor in complex with golimumab Fv
要素
  • Golimumab heavy chain variable region
  • Golimumab light chain variable region
  • Tumor necrosis factor
キーワードIMMUNE SYSTEM / Cytokine / Antibody
機能・相同性
機能・相同性情報


negative regulation of L-glutamate import across plasma membrane / negative regulation of branching involved in lung morphogenesis / negative regulation of bile acid secretion / response to Gram-negative bacterium / positive regulation of interleukin-33 production / positive regulation of neutrophil activation / positive regulation of blood microparticle formation / negative regulation of signaling receptor activity / positive regulation of chronic inflammatory response to antigenic stimulus / positive regulation of fractalkine production ...negative regulation of L-glutamate import across plasma membrane / negative regulation of branching involved in lung morphogenesis / negative regulation of bile acid secretion / response to Gram-negative bacterium / positive regulation of interleukin-33 production / positive regulation of neutrophil activation / positive regulation of blood microparticle formation / negative regulation of signaling receptor activity / positive regulation of chronic inflammatory response to antigenic stimulus / positive regulation of fractalkine production / positive regulation of leukocyte adhesion to arterial endothelial cell / positive regulation of vitamin D biosynthetic process / positive regulation of translational initiation by iron / response to macrophage colony-stimulating factor / regulation of membrane lipid metabolic process / regulation of endothelial cell apoptotic process / chronic inflammatory response to antigenic stimulus / regulation of branching involved in salivary gland morphogenesis / negative regulation of protein-containing complex disassembly / response to 3,3',5-triiodo-L-thyronine / response to gold nanoparticle / positive regulation of humoral immune response mediated by circulating immunoglobulin / positive regulation of hair follicle development / negative regulation of myelination / negative regulation of bicellular tight junction assembly / negative regulation of cytokine production involved in immune response / negative regulation of vascular wound healing / : / negative regulation of amyloid-beta clearance / response to isolation stress / positive regulation of action potential / inflammatory response to wounding / positive regulation of interleukin-18 production / death receptor agonist activity / positive regulation of protein transport / TNF signaling / epithelial cell proliferation involved in salivary gland morphogenesis / toll-like receptor 3 signaling pathway / embryonic digestive tract development / vascular endothelial growth factor production / leukocyte migration involved in inflammatory response / necroptotic signaling pathway / response to fructose / positive regulation of neuroinflammatory response / positive regulation of synoviocyte proliferation / positive regulation of calcineurin-NFAT signaling cascade / leukocyte tethering or rolling / positive regulation of mononuclear cell migration / positive regulation of fever generation / negative regulation of myoblast differentiation / cellular response to toxic substance / regulation of establishment of endothelial barrier / endothelial cell apoptotic process / negative regulation of D-glucose import / negative regulation of oxidative phosphorylation / positive regulation of protein localization to cell surface / macrophage activation involved in immune response / positive regulation of osteoclast differentiation / tumor necrosis factor receptor binding / positive regulation of protein-containing complex disassembly / negative regulation of systemic arterial blood pressure / positive regulation of heterotypic cell-cell adhesion / positive regulation of cytokine production involved in inflammatory response / positive regulation of macrophage derived foam cell differentiation / regulation of immunoglobulin production / TNFR1-mediated ceramide production / positive regulation of programmed cell death / positive regulation of hepatocyte proliferation / positive regulation of membrane protein ectodomain proteolysis / positive regulation of chemokine (C-X-C motif) ligand 2 production / positive regulation of extrinsic apoptotic signaling pathway / positive regulation of podosome assembly / regulation of canonical NF-kappaB signal transduction / regulation of fat cell differentiation / TNFR1-induced proapoptotic signaling / positive regulation of leukocyte adhesion to vascular endothelial cell / regulation of metabolic process / regulation of reactive oxygen species metabolic process / negative regulation of heart rate / positive regulation of amyloid-beta formation / positive regulation of DNA biosynthetic process / negative regulation of viral genome replication / response to L-glutamate / negative regulation of fat cell differentiation / regulation of synapse organization / Interleukin-10 signaling / negative regulation of endothelial cell proliferation / negative regulation of interleukin-6 production / negative regulation of blood vessel endothelial cell migration / humoral immune response / negative regulation of apoptotic signaling pathway / negative regulation of lipid storage / negative regulation of mitotic cell cycle / extrinsic apoptotic signaling pathway via death domain receptors / positive regulation of JUN kinase activity / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / cell surface receptor signaling pathway via JAK-STAT / phagocytic cup / negative regulation of osteoblast differentiation / positive regulation of synaptic transmission
類似検索 - 分子機能
Tumour necrosis factor alpha / Tumour necrosis factor / Tumour necrosis factor, conserved site / Tumor necrosis factor (TNF) homology domain (THD) signature. / Tumour necrosis factor family. / TNF(Tumour Necrosis Factor) family / Tumour necrosis factor domain / Tumor necrosis factor (TNF) homology domain (THD) profile. / Jelly Rolls - #40 / Tumour necrosis factor-like domain superfamily ...Tumour necrosis factor alpha / Tumour necrosis factor / Tumour necrosis factor, conserved site / Tumor necrosis factor (TNF) homology domain (THD) signature. / Tumour necrosis factor family. / TNF(Tumour Necrosis Factor) family / Tumour necrosis factor domain / Tumor necrosis factor (TNF) homology domain (THD) profile. / Jelly Rolls - #40 / Tumour necrosis factor-like domain superfamily / Jelly Rolls / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
類似検索 - ドメイン・相同性
Tumor necrosis factor
類似検索 - 構成要素
生物種Homo sapiens (ヒト)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 2.727 Å
データ登録者Ono, M. / Horita, S. / Sato, Y. / Nomura, Y. / Iwata, S. / Nomura, N.
資金援助 日本, 4件
組織認可番号国
Japan Science and Technology 日本
Japan Society for the Promotion of Science15K06968 日本
Japan Society for the Promotion of Science15J04343 日本
Japan Agency of Medical Research and Development 日本
引用ジャーナル: Protein Sci. / 年: 2018
タイトル: Structural basis for tumor necrosis factor blockade with the therapeutic antibody golimumab
著者: Ono, M. / Horita, S. / Sato, Y. / Nomura, Y. / Iwata, S. / Nomura, N.
履歴
登録2017年10月31日登録サイト: PDBJ / 処理サイト: PDBJ
改定 1.02018年5月9日Provider: repository / タイプ: Initial release
改定 1.12018年6月20日Group: Data collection / Database references / カテゴリ: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
改定 1.22018年11月14日Group: Data collection / Derived calculations
カテゴリ: pdbx_struct_assembly / pdbx_struct_assembly_gen
改定 1.32023年11月22日Group: Data collection / Database references / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
改定 1.42024年11月6日Group: Structure summary
カテゴリ: pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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構造の表示

構造ビューア分子:
MolmilJmol/JSmol

ダウンロードとリンク

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集合体

登録構造単位
A: Tumor necrosis factor
B: Tumor necrosis factor
C: Tumor necrosis factor
D: Golimumab light chain variable region
E: Golimumab light chain variable region
F: Golimumab light chain variable region
G: Golimumab heavy chain variable region
H: Golimumab heavy chain variable region
I: Golimumab heavy chain variable region
J: Tumor necrosis factor
K: Tumor necrosis factor
L: Tumor necrosis factor
M: Golimumab light chain variable region
N: Golimumab light chain variable region
O: Golimumab light chain variable region
P: Golimumab heavy chain variable region
Q: Golimumab heavy chain variable region
R: Golimumab heavy chain variable region


分子量 (理論値)分子数
合計 (水以外)279,32318
ポリマ－279,32318
非ポリマー00
水1,54986
1
A: Tumor necrosis factor
B: Tumor necrosis factor
C: Tumor necrosis factor
D: Golimumab light chain variable region
E: Golimumab light chain variable region
F: Golimumab light chain variable region
G: Golimumab heavy chain variable region
H: Golimumab heavy chain variable region
I: Golimumab heavy chain variable region


分子量 (理論値)分子数
合計 (水以外)139,6629
ポリマ－139,6629
非ポリマー00
水1629
タイプ名称対称操作数
identity operation1_555x,y,z1
2
J: Tumor necrosis factor
K: Tumor necrosis factor
L: Tumor necrosis factor
M: Golimumab light chain variable region
N: Golimumab light chain variable region
O: Golimumab light chain variable region
P: Golimumab heavy chain variable region
Q: Golimumab heavy chain variable region
R: Golimumab heavy chain variable region


分子量 (理論値)分子数
合計 (水以外)139,6629
ポリマ－139,6629
非ポリマー00
水1448
タイプ名称対称操作数
identity operation1_555x,y,z1
単位格子
Length a, b, c (Å)133.640, 85.300, 135.960
Angle α, β, γ (deg.)90.000, 101.610, 90.000
Int Tables number4
Space group name H-MP1211
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID詳細
11(chain G and (resseq 1:12 or resseq 14:39 or (resid...
21(chain H and (resseq 1:12 or resseq 14:39 or (resid...
31(chain I and (resseq 1:12 or resseq 14:39 or (resid...
41(chain P and (resseq 1:12 or resseq 14:39 or (resid...
51(chain Q and (resseq 1:12 or resseq 14:39 or (resid...
61(chain R and (resseq 1:12 or resseq 14:39 or (resid...
12(chain A and (resseq 11:24 or (resid 26 and (name...
22(chain B and (resseq 11:24 or (resid 26 and (name...
32(chain C and (resseq 11:24 or (resid 26 and (name...
42(chain J and (resseq 11:24 or (resid 26 and (name...
52(chain K and (resseq 11:24 or (resid 26 and (name...
62(chain L and (resseq 11:24 or (resid 26 and (name...
13(chain D and (resseq 1:10 or (resid 11 and (name...
23(chain E and (resseq 1:10 or (resid 11 and (name...
33(chain F and (resseq 1:10 or (resid 11 and (name...
43(chain M and (resseq 1:10 or (resid 11 and (name...
53(chain N and (resseq 1:10 or (resid 11 and (name...
63(chain O and (resseq 1:10 or (resid 11 and (name...

NCSドメイン領域:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111GLNGLNVALVAL(chain G and (resseq 1:12 or resseq 14:39 or (resid...GG1 - 124 - 15
121PROPROGLNGLN(chain G and (resseq 1:12 or resseq 14:39 or (resid...GG14 - 3917 - 42
131ALAALAALAALA(chain G and (resseq 1:12 or resseq 14:39 or (resid...GG4043
141GLNGLNSERSER(chain G and (resseq 1:12 or resseq 14:39 or (resid...GG1 - 1264 - 129
151GLNGLNSERSER(chain G and (resseq 1:12 or resseq 14:39 or (resid...GG1 - 1264 - 129
211GLNGLNVALVAL(chain H and (resseq 1:12 or resseq 14:39 or (resid...HH1 - 124 - 15
221PROPROGLNGLN(chain H and (resseq 1:12 or resseq 14:39 or (resid...HH14 - 3917 - 42
231ALAALAALAALA(chain H and (resseq 1:12 or resseq 14:39 or (resid...HH4043
241GLNGLNSERSER(chain H and (resseq 1:12 or resseq 14:39 or (resid...HH1 - 1264 - 129
251GLNGLNSERSER(chain H and (resseq 1:12 or resseq 14:39 or (resid...HH1 - 1264 - 129
311GLNGLNVALVAL(chain I and (resseq 1:12 or resseq 14:39 or (resid...II1 - 124 - 15
321PROPROGLNGLN(chain I and (resseq 1:12 or resseq 14:39 or (resid...II14 - 3917 - 42
331ALAALAALAALA(chain I and (resseq 1:12 or resseq 14:39 or (resid...II4043
341GLNGLNSERSER(chain I and (resseq 1:12 or resseq 14:39 or (resid...II1 - 1254 - 128
351GLNGLNSERSER(chain I and (resseq 1:12 or resseq 14:39 or (resid...II1 - 1254 - 128
411GLNGLNVALVAL(chain P and (resseq 1:12 or resseq 14:39 or (resid...PP1 - 124 - 15
421PROPROGLNGLN(chain P and (resseq 1:12 or resseq 14:39 or (resid...PP14 - 3917 - 42
431ALAALAALAALA(chain P and (resseq 1:12 or resseq 14:39 or (resid...PP4043
441GLNGLNSERSER(chain P and (resseq 1:12 or resseq 14:39 or (resid...PP1 - 1264 - 129
451GLNGLNSERSER(chain P and (resseq 1:12 or resseq 14:39 or (resid...PP1 - 1264 - 129
511GLNGLNVALVAL(chain Q and (resseq 1:12 or resseq 14:39 or (resid...QQ1 - 124 - 15
521PROPROGLNGLN(chain Q and (resseq 1:12 or resseq 14:39 or (resid...QQ14 - 3917 - 42
531ALAALAALAALA(chain Q and (resseq 1:12 or resseq 14:39 or (resid...QQ4043
541GLNGLNSERSER(chain Q and (resseq 1:12 or resseq 14:39 or (resid...QQ1 - 1264 - 129
551GLNGLNSERSER(chain Q and (resseq 1:12 or resseq 14:39 or (resid...QQ1 - 1264 - 129
611GLNGLNVALVAL(chain R and (resseq 1:12 or resseq 14:39 or (resid...RR1 - 124 - 15
621PROPROGLNGLN(chain R and (resseq 1:12 or resseq 14:39 or (resid...RR14 - 3917 - 42
631ALAALAALAALA(chain R and (resseq 1:12 or resseq 14:39 or (resid...RR4043
641GLNGLNSERSER(chain R and (resseq 1:12 or resseq 14:39 or (resid...RR1 - 1264 - 129
651GLNGLNSERSER(chain R and (resseq 1:12 or resseq 14:39 or (resid...RR1 - 1264 - 129
112LYSLYSGLYGLY(chain A and (resseq 11:24 or (resid 26 and (name...AA11 - 2419 - 32
122LEULEULEULEU(chain A and (resseq 11:24 or (resid 26 and (name...AA2634
132ARGARGSERSER(chain A and (resseq 11:24 or (resid 26 and (name...AA6 - 15914 - 167
142ARGARGSERSER(chain A and (resseq 11:24 or (resid 26 and (name...AA6 - 15914 - 167
152ARGARGSERSER(chain A and (resseq 11:24 or (resid 26 and (name...AA6 - 15914 - 167
162ARGARGSERSER(chain A and (resseq 11:24 or (resid 26 and (name...AA6 - 15914 - 167
172ARGARGSERSER(chain A and (resseq 11:24 or (resid 26 and (name...AA6 - 15914 - 167
182ARGARGSERSER(chain A and (resseq 11:24 or (resid 26 and (name...AA6 - 15914 - 167
212LYSLYSGLYGLY(chain B and (resseq 11:24 or (resid 26 and (name...BB11 - 2419 - 32
222LEULEULEULEU(chain B and (resseq 11:24 or (resid 26 and (name...BB2634
232ARGARGSERSER(chain B and (resseq 11:24 or (resid 26 and (name...BB6 - 15914 - 167
242ARGARGSERSER(chain B and (resseq 11:24 or (resid 26 and (name...BB6 - 15914 - 167
252ARGARGSERSER(chain B and (resseq 11:24 or (resid 26 and (name...BB6 - 15914 - 167
262ARGARGSERSER(chain B and (resseq 11:24 or (resid 26 and (name...BB6 - 15914 - 167
272ARGARGSERSER(chain B and (resseq 11:24 or (resid 26 and (name...BB6 - 15914 - 167
282ARGARGSERSER(chain B and (resseq 11:24 or (resid 26 and (name...BB6 - 15914 - 167
312LYSLYSGLYGLY(chain C and (resseq 11:24 or (resid 26 and (name...CC11 - 2419 - 32
322LEULEULEULEU(chain C and (resseq 11:24 or (resid 26 and (name...CC2634
332ARGARGSERSER(chain C and (resseq 11:24 or (resid 26 and (name...CC6 - 15914 - 167
342ARGARGSERSER(chain C and (resseq 11:24 or (resid 26 and (name...CC6 - 15914 - 167
352ARGARGSERSER(chain C and (resseq 11:24 or (resid 26 and (name...CC6 - 15914 - 167
362ARGARGSERSER(chain C and (resseq 11:24 or (resid 26 and (name...CC6 - 15914 - 167
372ARGARGSERSER(chain C and (resseq 11:24 or (resid 26 and (name...CC6 - 15914 - 167
382ARGARGSERSER(chain C and (resseq 11:24 or (resid 26 and (name...CC6 - 15914 - 167
412LYSLYSGLYGLY(chain J and (resseq 11:24 or (resid 26 and (name...JJ11 - 2419 - 32
422LEULEULEULEU(chain J and (resseq 11:24 or (resid 26 and (name...JJ2634
432ARGARGTHRTHR(chain J and (resseq 11:24 or (resid 26 and (name...JJ6 - 15814 - 166
442ARGARGTHRTHR(chain J and (resseq 11:24 or (resid 26 and (name...JJ6 - 15814 - 166
452ARGARGTHRTHR(chain J and (resseq 11:24 or (resid 26 and (name...JJ6 - 15814 - 166
462ARGARGTHRTHR(chain J and (resseq 11:24 or (resid 26 and (name...JJ6 - 15814 - 166
472ARGARGTHRTHR(chain J and (resseq 11:24 or (resid 26 and (name...JJ6 - 15814 - 166
482ARGARGTHRTHR(chain J and (resseq 11:24 or (resid 26 and (name...JJ6 - 15814 - 166
512LYSLYSGLYGLY(chain K and (resseq 11:24 or (resid 26 and (name...KK11 - 2419 - 32
522LEULEULEULEU(chain K and (resseq 11:24 or (resid 26 and (name...KK2634
532ARGARGTHRTHR(chain K and (resseq 11:24 or (resid 26 and (name...KK6 - 15814 - 166
542ARGARGTHRTHR(chain K and (resseq 11:24 or (resid 26 and (name...KK6 - 15814 - 166
552ARGARGTHRTHR(chain K and (resseq 11:24 or (resid 26 and (name...KK6 - 15814 - 166
562ARGARGTHRTHR(chain K and (resseq 11:24 or (resid 26 and (name...KK6 - 15814 - 166
572ARGARGTHRTHR(chain K and (resseq 11:24 or (resid 26 and (name...KK6 - 15814 - 166
582ARGARGTHRTHR(chain K and (resseq 11:24 or (resid 26 and (name...KK6 - 15814 - 166
612LYSLYSGLYGLY(chain L and (resseq 11:24 or (resid 26 and (name...LL11 - 2419 - 32
622LEULEULEULEU(chain L and (resseq 11:24 or (resid 26 and (name...LL2634
632ARGARGTHRTHR(chain L and (resseq 11:24 or (resid 26 and (name...LL6 - 15814 - 166
642ARGARGTHRTHR(chain L and (resseq 11:24 or (resid 26 and (name...LL6 - 15814 - 166
652ARGARGTHRTHR(chain L and (resseq 11:24 or (resid 26 and (name...LL6 - 15814 - 166
662ARGARGTHRTHR(chain L and (resseq 11:24 or (resid 26 and (name...LL6 - 15814 - 166
672ARGARGTHRTHR(chain L and (resseq 11:24 or (resid 26 and (name...LL6 - 15814 - 166
682ARGARGTHRTHR(chain L and (resseq 11:24 or (resid 26 and (name...LL6 - 15814 - 166
113GLUGLUTHRTHR(chain D and (resseq 1:10 or (resid 11 and (name...DD1 - 104 - 13
123LEULEULEULEU(chain D and (resseq 1:10 or (resid 11 and (name...DD1114
133GLUGLULYSLYS(chain D and (resseq 1:10 or (resid 11 and (name...DD1 - 1084 - 111
143GLUGLULYSLYS(chain D and (resseq 1:10 or (resid 11 and (name...DD1 - 1084 - 111
153GLUGLULYSLYS(chain D and (resseq 1:10 or (resid 11 and (name...DD1 - 1084 - 111
163GLUGLULYSLYS(chain D and (resseq 1:10 or (resid 11 and (name...DD1 - 1084 - 111
173GLUGLULYSLYS(chain D and (resseq 1:10 or (resid 11 and (name...DD1 - 1084 - 111
183GLUGLULYSLYS(chain D and (resseq 1:10 or (resid 11 and (name...DD1 - 1084 - 111
213GLUGLUTHRTHR(chain E and (resseq 1:10 or (resid 11 and (name...EE1 - 104 - 13
223LEULEULEULEU(chain E and (resseq 1:10 or (resid 11 and (name...EE1114
233GLUGLULYSLYS(chain E and (resseq 1:10 or (resid 11 and (name...EE1 - 1084 - 111
243GLUGLULYSLYS(chain E and (resseq 1:10 or (resid 11 and (name...EE1 - 1084 - 111
253GLUGLULYSLYS(chain E and (resseq 1:10 or (resid 11 and (name...EE1 - 1084 - 111
263GLUGLULYSLYS(chain E and (resseq 1:10 or (resid 11 and (name...EE1 - 1084 - 111
273GLUGLULYSLYS(chain E and (resseq 1:10 or (resid 11 and (name...EE1 - 1084 - 111
283GLUGLULYSLYS(chain E and (resseq 1:10 or (resid 11 and (name...EE1 - 1084 - 111
313GLUGLUTHRTHR(chain F and (resseq 1:10 or (resid 11 and (name...FF1 - 104 - 13
323LEULEULEULEU(chain F and (resseq 1:10 or (resid 11 and (name...FF1114
333GLUGLULYSLYS(chain F and (resseq 1:10 or (resid 11 and (name...FF1 - 1084 - 111
343GLUGLULYSLYS(chain F and (resseq 1:10 or (resid 11 and (name...FF1 - 1084 - 111
353GLUGLULYSLYS(chain F and (resseq 1:10 or (resid 11 and (name...FF1 - 1084 - 111
363GLUGLULYSLYS(chain F and (resseq 1:10 or (resid 11 and (name...FF1 - 1084 - 111
373GLUGLULYSLYS(chain F and (resseq 1:10 or (resid 11 and (name...FF1 - 1084 - 111
383GLUGLULYSLYS(chain F and (resseq 1:10 or (resid 11 and (name...FF1 - 1084 - 111
413GLUGLUTHRTHR(chain M and (resseq 1:10 or (resid 11 and (name...MM1 - 104 - 13
423LEULEULEULEU(chain M and (resseq 1:10 or (resid 11 and (name...MM1114
433GLUGLULYSLYS(chain M and (resseq 1:10 or (resid 11 and (name...MM1 - 1084 - 111
443GLUGLULYSLYS(chain M and (resseq 1:10 or (resid 11 and (name...MM1 - 1084 - 111
453GLUGLULYSLYS(chain M and (resseq 1:10 or (resid 11 and (name...MM1 - 1084 - 111
463GLUGLULYSLYS(chain M and (resseq 1:10 or (resid 11 and (name...MM1 - 1084 - 111
473GLUGLULYSLYS(chain M and (resseq 1:10 or (resid 11 and (name...MM1 - 1084 - 111
483GLUGLULYSLYS(chain M and (resseq 1:10 or (resid 11 and (name...MM1 - 1084 - 111
513GLUGLUTHRTHR(chain N and (resseq 1:10 or (resid 11 and (name...NN1 - 104 - 13
523LEULEULEULEU(chain N and (resseq 1:10 or (resid 11 and (name...NN1114
533GLUGLULYSLYS(chain N and (resseq 1:10 or (resid 11 and (name...NN1 - 1084 - 111
543GLUGLULYSLYS(chain N and (resseq 1:10 or (resid 11 and (name...NN1 - 1084 - 111
553GLUGLULYSLYS(chain N and (resseq 1:10 or (resid 11 and (name...NN1 - 1084 - 111
563GLUGLULYSLYS(chain N and (resseq 1:10 or (resid 11 and (name...NN1 - 1084 - 111
573GLUGLULYSLYS(chain N and (resseq 1:10 or (resid 11 and (name...NN1 - 1084 - 111
583GLUGLULYSLYS(chain N and (resseq 1:10 or (resid 11 and (name...NN1 - 1084 - 111
613GLUGLUTHRTHR(chain O and (resseq 1:10 or (resid 11 and (name...OO1 - 104 - 13
623LEULEULEULEU(chain O and (resseq 1:10 or (resid 11 and (name...OO1114
633GLUGLULYSLYS(chain O and (resseq 1:10 or (resid 11 and (name...OO1 - 1084 - 111
643GLUGLULYSLYS(chain O and (resseq 1:10 or (resid 11 and (name...OO1 - 1084 - 111
653GLUGLULYSLYS(chain O and (resseq 1:10 or (resid 11 and (name...OO1 - 1084 - 111
663GLUGLULYSLYS(chain O and (resseq 1:10 or (resid 11 and (name...OO1 - 1084 - 111
673GLUGLULYSLYS(chain O and (resseq 1:10 or (resid 11 and (name...OO1 - 1084 - 111
683GLUGLULYSLYS(chain O and (resseq 1:10 or (resid 11 and (name...OO1 - 1084 - 111

NCSアンサンブル:
ID
1
2
3

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要素

#1: タンパク質
Tumor necrosis factor / Cachectin / TNF-alpha / Tumor necrosis factor ligand superfamily member 2 / TNF-a


分子量: 19350.666 Da / 分子数: 6 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: TNF, TNFA, TNFSF2 / 発現宿主: Brevibacillus choshinensis (バクテリア) / 参照: UniProt: P01375
#2: 抗体
Golimumab light chain variable region


分子量: 13022.391 Da / 分子数: 6 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 発現宿主: Brevibacillus choshinensis (バクテリア)
#3: 抗体
Golimumab heavy chain variable region


分子量: 14180.830 Da / 分子数: 6 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 発現宿主: Brevibacillus choshinensis (バクテリア)
#4: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 86 / 由来タイプ: 天然 / 式: H2O
Has protein modificationY
配列の詳細AUTHORS STATE THAT 158THR/159SER ARE DUE TO RISTRICTION ENZYME, AND ...AUTHORS STATE THAT 158THR/159SER ARE DUE TO RISTRICTION ENZYME, AND 160GLU/161ASN/162LEU/163TYR/164PHE/165GLN ARE DUE TO PROTEASE CLEAVAGE.

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実験情報

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実験

実験手法: X線回折 / 使用した結晶の数: 1

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試料調製

結晶マシュー密度: 2.96 Å3/Da / 溶媒含有率: 58.47 %
結晶化温度: 293 K / 手法: 蒸気拡散法, ハンギングドロップ法
詳細: 0.1M sodium acetate trihydrate pH 4.6, 1.4M sodium chloride

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データ収集

回折平均測定温度: 100 K
放射光源由来: シンクロトロン / サイト: SPring-8 / ビームライン: BL41XU / 波長: 1 Å
検出器タイプ: DECTRIS PILATUS3 6M / 検出器: PIXEL / 日付: 2016年10月8日
放射プロトコル: SINGLE WAVELENGTH / 単色(M)・ラウエ(L): M / 散乱光タイプ: x-ray
放射波長波長: 1 Å / 相対比: 1
反射解像度: 2.73→46.25 Å / Num. obs: 77915 / % possible obs: 97.1 % / Observed criterion σ(I): -3 / 冗長度: 3.428 % / CC1/2: 0.993 / Rmerge(I) obs: 0.107 / Rrim(I) all: 0.127 / Χ2: 1.067 / Net I/σ(I): 9.47 / Num. measured all: 267101 / Scaling rejects: 2
反射 シェル

Diffraction-ID: 1

解像度 (Å)冗長度 (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.73-2.83.520.9881.4819144586354390.5391.16392.8
2.8-2.873.5510.8231.8820094576256590.6150.9798.2
2.87-2.963.4790.6462.4119181560755140.7410.76498.3
2.96-3.053.4480.5693.0518624548154010.8170.67498.5
3.05-3.153.3550.4293.9817173522751190.8530.51197.9
3.15-3.263.2360.3115.1615890510749100.9030.37396.1
3.26-3.383.6090.2646.6617369489748130.9560.3198.3
3.38-3.523.5530.1848.7216676477146930.9730.21798.4
3.52-3.683.4980.14310.315669455544800.9810.16998.4
3.68-3.863.4780.11611.7414823433642620.9850.13798.3
3.86-4.073.3540.09213.413629416240630.9880.10997.6
4.07-4.313.1710.07215.0511711391536930.9910.08694.3
4.31-4.613.5290.06517.8312662368935880.9920.07797.3
4.61-4.983.4720.06218.3711699345133700.9920.07497.7
4.98-5.453.4270.06118.3210525317830710.9920.07296.6
5.45-6.13.1990.06516.498896289027810.9910.07996.2
6.1-7.043.3210.06317.478051254824240.9910.07595.1
7.04-8.623.3970.05519.557184215721150.9930.06598.1
8.62-12.23.1640.04820.825100171416120.9940.05794
12.2-46.253.3050.04621.4630019599080.9970.05594.7

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解析

ソフトウェア
名称バージョン分類
PHENIXdev_2210精密化
XSCALEデータスケーリング
PDB_EXTRACT3.22データ抽出
XDSデータ削減
PHASER位相決定
精密化構造決定の手法: 分子置換
開始モデル: 1A8M, 5B8C

1a8m

5b8c


解像度: 2.727→46.25 Å / SU ML: 0.43 / 交差検証法: FREE R-VALUE / σ(F): 1.37 / 位相誤差: 25.88 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.2335 3936 5.05 %
Rwork0.19 73966 -
obs0.1922 77902 97.11 %
溶媒の処理減衰半径: 0.9 Å / VDWプローブ半径: 1.11 Å / 溶媒モデル: FLAT BULK SOLVENT MODEL
原子変位パラメータBiso max: 213.52 Å2 / Biso mean: 77.8314 Å2 / Biso min: 33.46 Å2
精密化ステップサイクル: final / 解像度: 2.727→46.25 Å
タンパク質核酸リガンド溶媒全体
原子数18030 0 0 86 18116
Biso mean---59.3 -
残基数----2324
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00318480
X-RAY DIFFRACTIONf_angle_d0.67225132
X-RAY DIFFRACTIONf_chiral_restr0.0472714
X-RAY DIFFRACTIONf_plane_restr0.0053266
X-RAY DIFFRACTIONf_dihedral_angle_d14.06810964
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-ID数Refine-IDRmsタイプ
11G3306X-RAY DIFFRACTION10.295TORSIONAL
12H3306X-RAY DIFFRACTION10.295TORSIONAL
13I3306X-RAY DIFFRACTION10.295TORSIONAL
14P3306X-RAY DIFFRACTION10.295TORSIONAL
15Q3306X-RAY DIFFRACTION10.295TORSIONAL
16R3306X-RAY DIFFRACTION10.295TORSIONAL
21A3735X-RAY DIFFRACTION10.295TORSIONAL
22B3735X-RAY DIFFRACTION10.295TORSIONAL
23C3735X-RAY DIFFRACTION10.295TORSIONAL
24J3735X-RAY DIFFRACTION10.295TORSIONAL
25K3735X-RAY DIFFRACTION10.295TORSIONAL
26L3735X-RAY DIFFRACTION10.295TORSIONAL
31D2851X-RAY DIFFRACTION10.295TORSIONAL
32E2851X-RAY DIFFRACTION10.295TORSIONAL
33F2851X-RAY DIFFRACTION10.295TORSIONAL
34M2851X-RAY DIFFRACTION10.295TORSIONAL
35N2851X-RAY DIFFRACTION10.295TORSIONAL
36O2851X-RAY DIFFRACTION10.295TORSIONAL
LS精密化 シェル

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 28

解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.7273-2.76060.39911320.35432325245787
2.7606-2.79550.34441420.34412639278199
2.7955-2.83230.3341280.3172711283998
2.8323-2.87110.36431430.3232615275898
2.8711-2.91210.35261520.30852659281198
2.9121-2.95550.32771540.29542648280298
2.9555-3.00170.31381370.27482649278699
3.0017-3.05090.31181390.26532725286499
3.0509-3.10350.25461610.25782600276198
3.1035-3.15990.31781460.2472637278397
3.1599-3.22070.31131270.24632567269495
3.2207-3.28640.27741410.23312665280698
3.2864-3.35790.30391270.23662657278498
3.3579-3.43590.27711330.22312687282098
3.4359-3.52180.26021550.21092667282298
3.5218-3.6170.2091190.19282676279598
3.617-3.72340.24961490.19162664281398
3.7234-3.84350.23151480.18992655280398
3.8435-3.98080.22771490.1792663281298
3.9808-4.14010.23341200.16742655277597
4.1401-4.32840.19461570.15232539269694
4.3284-4.55640.14831520.13762632278497
4.5564-4.84160.17831450.13352662280798
4.8416-5.2150.17071130.14082674278797
5.215-5.73890.19951300.15482683281397
5.7389-6.56730.2551410.17412605274694
6.5673-8.26650.2141600.17162681284198
8.2665-46.25680.20511360.16992726286295
精密化 TLS

手法: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
15.4107-4.09061.45926.438-0.32186.3688-1.43234.4586-1.9731-1.69750.7952-0.03850.51670.28540.56841.1467-0.2144-0.00771.5449-0.1370.4908223.8106-423.4674263.8461
22.32971.328-2.41476.94-2.17262.6055-0.4721.0689-0.1637-1.2822-0.7131-0.3239-0.00821.14721.21831.0663-0.409-0.12031.53170.17290.7542234.1807-416.2948266.4538
35.91320.31590.85512.4207-0.09744.2985-0.64971.48030.2294-0.8810.41160.1818-0.69990.52170.23530.7637-0.2973-0.08060.78770.13880.4341226.942-417.3419273.2406
45.54373.8161-1.90044.76052.80918.791-0.27590.80851.8715-0.6934-0.44120.9239-1.9585-0.35870.69570.9014-0.1148-0.25070.57870.10770.7398221.0608-410.4442279.5708
53.46570.57843.67122.2356-0.57165.5734-0.3619-1.4782-0.2402-0.10120.1532-0.3263-0.53260.1120.33290.5389-0.19170.00950.714-0.02070.4174237.4574-419.7152286.897
65.0172-1.59334.75683.5192-1.46794.9739-1.22630.16122.1007-0.5501-0.01160.629-0.9165-0.11941.1351.0683-0.1093-0.3240.91780.11880.6864219.2177-411.2056271.7682
73.15993.71132.77654.54011.98776.6882-0.45320.8782-0.1873-0.93220.5287-0.1773-0.3710.4746-0.01150.8291-0.280.00140.7858-0.00720.489230.6663-420.2124274.2422
88.91312.41141.83228.98996.26494.4025-1.04250.34251.067-0.6682-0.15581.1306-1.6121-2.11791.43670.83050.0319-0.19730.82570.05540.7117206.8902-419.9091284.3099
94.34354.54153.24387.41155.19013.62550.1446-0.63091.5093-0.5751-0.49560.5241-1.0275-2.53370.48820.67310.1196-0.01390.9358-0.21241.1103210.3764-417.0785294.7976
108.7773.14622.53513.34361.84827.5697-0.26310.28070.5695-0.2657-0.06310.9029-0.1293-1.17350.2360.5156-0.0293-0.04940.5713-0.02630.5157210.3176-425.4742287.5055
112.13192.06082.11122.04342.01712.051-0.4155-0.5246-1.4888-0.38470.4327-2.09461.3988-0.3539-0.40380.878-0.0294-0.02540.5507-0.03030.6298233.1549-424.8698305.6816
124.11211.51193.10182.47292.43673.7096-0.0049-1.20570.30870.561-0.3790.79330.5035-0.96880.34860.6754-0.18090.13080.5624-0.05060.5623214.7538-435.8385293.8675
136.70386.19917.98865.96897.37369.37490.02660.7717-1.24090.02630.7917-1.54380.18550.5229-0.9120.8179-0.0831-0.0090.6186-0.1140.6898239.6626-419.0647304.4465
148.02065.90556.01546.36473.48934.5571-1.16480.84660.1231-1.05830.8680.0741-0.58630.4920.41330.7686-0.20790.05970.6025-0.02380.3217222.7449-427.0076288.489
153.72313.18085.90863.25985.41329.71611.0852-0.122-0.00211.4256-0.8826-0.10311.4329-0.9584-0.30860.7715-0.2007-0.0060.6890.04450.5812208.0252-433.1749291.3468
168.42665.03964.97224.86743.9258.3461-0.72750.36340.4479-0.59730.43460.5459-0.9757-0.470.20130.5909-0.023-0.00350.43480.01580.3892217.5671-421.8483290.5519
177.5393-2.36384.42038.7036-2.02518.24420.70030.0576-1.851.1750.3510.4191.366-0.7027-1.08441.3667-0.3945-0.39850.78030.05471.0688221.1844-445.9109276.4929
184.9096-1.23583.46811.6814-2.11595.5899-0.01880.9624-0.3417-0.2233-0.0123-0.05420.10040.9139-0.0690.6265-0.11760.10760.6882-0.02560.4081234.723-434.8589280.6817
198.5843-3.10526.082.2366-1.9555.8286-0.0047-0.5391-0.53240.03290.36590.39760.5297-0.6692-0.49670.8377-0.24790.00860.64140.0490.4413227.5651-439.0577283.2196
202.02740.70651.02832.5333-1.4685.4714-0.0863-0.1821-0.29560.4559-0.10510.3806-0.1035-0.88590.17980.74120.08710.13380.4877-0.02570.5352216.9165-414.9264329.5358
215.3119-5.5708-6.8945.88287.26989.10811.40522.44780.2281-0.9028-1.50790.0107-0.0448-1.57940.07040.58470.07050.04010.6401-0.02010.4424217.8442-417.872311.8343
228.14724.2907-1.49784.4310.97934.06020.9231-0.57010.32920.8243-0.4204-0.1027-0.97050.2529-0.49270.8234-0.04170.02030.27390.01220.3899229.3887-410.1286326.6029
234.41410.7250.87894.13632.39322.1366-0.0077-0.0473-0.0820.1963-0.16160.1790.72830.11360.01160.6501-0.00020.08160.32180.06070.3512226.6884-420.6339324.4166
242.52840.0843.51113.6831-0.87425.1983-0.394-0.21610.24080.69091.3137-0.4522-0.3012-0.7485-0.22890.67120.0450.14690.45640.00450.4588228.633-415.6994338.491
252.6875-1.5184-0.71178.03344.6192.90610.01550.17470.025-0.0779-0.33950.5486-0.8442-0.37170.25720.6215-0.04860.00240.30590.05450.3532221.4715-409.103318.0764
264.0641-1.481-0.60352.90353.7575.38490.4562-1.76981.92690.70650.04480.3555-0.15541.3875-1.06241.15850.0163-0.00480.7629-0.12440.6447220.6145-409.7545340.5305
274.1413-3.4618-4.69416.62313.11145.2996-0.04441.453-1.7603-0.02210.3397-1.31180.43521.0138-0.20010.78730.0950.11370.8343-0.29981.1175258.3802-463.9353293.8358
284.4918-5.19735.62636.418-6.03818.0183-0.61161.4029-1.2568-1.1948-0.005-0.92631.03520.86830.5051.007-0.10520.38150.9406-0.25950.9707255.7021-460.6592290.2426
299.3132-0.75816.05879.63450.79684.3649-0.34860.7226-1.0554-0.24160.61070.2538-0.04830.4-0.21490.51670.00260.08250.7271-0.03320.5596249.8751-452.9487294.222
308.41913.3434-3.01719.0864-6.66755.04290.7032-0.4132-0.53150.0417-0.684-1.45130.9613.2206-0.08080.67510.1383-0.03830.8096-0.13160.7624259.7921-454.4704305.994
313.79843.29471.77915.4457-1.84135.22980.6648-0.43660.1623-0.24580.438-1.2041-0.62691.4193-1.01170.72630.03150.2091.0171-0.28910.859261.2556-446.6978296.306
325.01691.9304-3.03268.1143-2.92892.8788-0.30040.733-0.0715-0.44510.1761-1.46480.45691.28440.04990.74290.00210.18291.0919-0.30690.9224262.5482-456.3701294.0003
336.2104-6.34396.85796.4576-6.97377.62110.12810.5212-0.7413-0.99190.3404-1.00310.76850.524-0.45010.62340.01950.09470.6334-0.23290.9094253.2472-457.6704299.4898
343.788-4.2125-3.28588.39252.43283.0877-0.07430.04-0.6088-1.40980.64060.12750.80210.0418-0.53460.75530.00050.09090.642-0.03850.5655244.3664-455.1996298.3692
352.7421-0.5995-2.58716.88822.56023.0461-0.912-2.34331.3532.20180.8252-1.7134-0.25760.19720.12381.44190.3846-0.0310.9644-0.32911.3337266.0939-468.0101300.9747
367.7744-1.7756-4.18672.9717-1.01743.92990.24970.28810.8611-2.58120.0102-0.2211-0.53030.8707-0.3821.1362-0.20030.03741.0598-0.00620.6269252.3303-399.8167268.3076
375.12745.1791.8775.33712.10361.1068-0.04320.7584-0.4021-1.53570.931-1.2544-1.13990.2951-1.14961.7135-0.58980.5181.118-0.03151.2154260.6822-382.5997278.2654
388.45345.03616.03943.9064.2434.7839-1.71052.27941.985-2.38131.94840.7079-2.44230.4872-0.25511.4219-0.45650.18181.21640.38661.1987252.292-391.877274.8727
394.854-1.1224-2.87132.649-1.62033.8604-0.06390.92850.8958-1.0701-0.37770.19570.89930.4916-0.02191.3878-0.54060.12541.01930.27470.6249244.9705-404.5266274.829
406.90090.1882-4.24187.6658-1.9023.50080.1194-0.56120.51590.28540.0704-1.1728-0.24591.1963-0.09880.971-0.70870.39391.4418-0.2240.7995263.1609-399.1415282.0662
419.27595.07825.95537.77995.36274.74650.653-0.9006-0.45180.3297-0.2222-0.5944-0.7554-0.5346-0.43191.171-0.50690.26571.4537-0.20860.7276255.3198-397.6758289.6112
427.8958.08046.82318.46217.17268.3831-1.07391.792.26491.61790.83751.4592-0.94971.50160.1621.8187-0.3630.37680.904-0.10131.023250.9634-393.8548283.9115
439.91017.99168.06769.18587.73579.5316-1.18280.78592.1641-1.03230.88421.8959-2.14770.26290.50581.3816-0.37970.19280.85850.11171.1102250.093-393.3316278.7109
447.4995-6.1982-3.77165.34523.73713.8462-1.2280.2294-0.91730.5979-0.09050.2289-1.98582.05641.18641.4864-0.72610.22511.4677-0.06351.0985264.6795-386.576285.422
455.7783.717-0.36124.5172-0.43180.09870.68840.16351.88530.44650.11090.1661-1.33461.165-0.55290.2842-1.5161.3360.94240.3919-0.1084259.0745-399.2782276.4056
465.41781.9619-0.05673.0396-0.8140.88180.1660.266-0.01120.06450.2165-0.4951-0.93030.0601-0.50880.9797-0.46010.18131.0051-0.08990.5522254.763-406.6362272.7438
471.4481-3.99322.40991.9958-6.56983.9341-0.96440.7554-0.6892.2568-0.9158-1.12961.7113-1.4105-0.3371.8106-0.56960.36351.2411-0.37160.9193267.0889-383.898276.2207
488.8262-3.67531.43768.40962.81263.0935-0.2163-0.34690.45570.11770.23240.1998-0.88330.12120.20760.8736-0.09320.15450.35520.04690.4719234.6101-390.1909319.4458
495.7006-6.4315-1.25977.44091.40840.27830.5232-0.4613-0.08320.32780.1115-0.0031-1.03560.6215-0.36651.1959-0.05450.12670.29110.01070.6282238.1685-393.2192315.1974
504.0713-1.44530.79572.8731-0.20240.7514-0.30830.278-0.16170.22980.1365-0.0883-0.26310.06450.17240.685-0.052-0.01340.3514-0.01260.3397236.164-403.1344314.0266
512.58270.61580.7533.35683.3863.41930.52410.1450.4230.2254-0.37360.4903-0.6614-0.88710.06760.75730.01760.00660.2880.03030.4849224.7595-400.1124317.929
527.7249-1.6172-4.07973.9781.04132.9101-0.28891.4450.4728-1.01150.2397-0.4921-0.0117-0.7574-0.06430.8852-0.0088-0.12980.51240.12070.4986231.6174-402.9388303.5085
535.9696-0.9050.33354.2054-0.60553.40050.19480.43060.4435-0.5188-0.0989-0.0526-0.6295-0.0283-0.09910.88930.00980.06160.36240.05460.4969232.3505-394.5277309.4351
548.0918-7.2299-4.55726.20334.02436.3830.09180.3443-0.16210.4986-0.26920.7232-0.5821-0.42050.12330.9206-0.0720.08260.40420.02830.5386227.035-394.1485317.8202
555.21184.44534.44795.22456.21879.4891-0.11480.34810.04670.4771-0.01170.11580.40140.60340.09320.64170.00640.01040.31130.04740.361231.412-411.0244312.9409
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1343.9863-2.20222.24229.6735-0.60682.12150.1094-0.01460.55570.2525-0.01790.4242-1.58240.6220.28411.2783-0.150.12740.3826-0.13790.7003267.8905-387.0533207.6852
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1385.9535-0.15783.04536.2312-0.23894.6231-0.6513-0.87990.67051.53410.1592-0.3549-0.20840.52940.44231.07330.255-0.20850.7569-0.03920.7482268.9452-433.9028260.307
1398.3892-1.64454.46234.4829-0.75885.5102-0.07740.29830.24260.5642-0.1-0.34740.04570.6822-0.05320.70120.20760.10710.76310.14080.5136261.9535-440.6709246.8421
1404.6938-0.18760.73251.75561.34011.192-0.3086-0.27590.13231.17830.16160.6075-0.1221.5617-0.2261.87530.5519-0.43951.2668-0.13750.9441276.014-440.6632270.3653
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 6 through 22 )A6 - 22
2X-RAY DIFFRACTION2chain 'A' and (resid 23 through 32 )A23 - 32
3X-RAY DIFFRACTION3chain 'A' and (resid 33 through 75 )A33 - 75
4X-RAY DIFFRACTION4chain 'A' and (resid 76 through 98 )A76 - 98
5X-RAY DIFFRACTION5chain 'A' and (resid 99 through 126 )A99 - 126
6X-RAY DIFFRACTION6chain 'A' and (resid 127 through 136 )A127 - 136
7X-RAY DIFFRACTION7chain 'A' and (resid 137 through 159 )A137 - 159
8X-RAY DIFFRACTION8chain 'B' and (resid 6 through 22 )B6 - 22
9X-RAY DIFFRACTION9chain 'B' and (resid 23 through 32 )B23 - 32
10X-RAY DIFFRACTION10chain 'B' and (resid 33 through 67 )B33 - 67
11X-RAY DIFFRACTION11chain 'B' and (resid 68 through 75 )B68 - 75
12X-RAY DIFFRACTION12chain 'B' and (resid 76 through 98 )B76 - 98
13X-RAY DIFFRACTION13chain 'B' and (resid 99 through 112 )B99 - 112
14X-RAY DIFFRACTION14chain 'B' and (resid 113 through 126 )B113 - 126
15X-RAY DIFFRACTION15chain 'B' and (resid 127 through 136 )B127 - 136
16X-RAY DIFFRACTION16chain 'B' and (resid 137 through 159 )B137 - 159
17X-RAY DIFFRACTION17chain 'C' and (resid 6 through 53 )C6 - 53
18X-RAY DIFFRACTION18chain 'C' and (resid 54 through 136 )C54 - 136
19X-RAY DIFFRACTION19chain 'C' and (resid 137 through 159 )C137 - 159
20X-RAY DIFFRACTION20chain 'D' and (resid 1 through 25 )D1 - 25
21X-RAY DIFFRACTION21chain 'D' and (resid 26 through 32 )D26 - 32
22X-RAY DIFFRACTION22chain 'D' and (resid 33 through 48 )D33 - 48
23X-RAY DIFFRACTION23chain 'D' and (resid 49 through 75 )D49 - 75
24X-RAY DIFFRACTION24chain 'D' and (resid 76 through 84 )D76 - 84
25X-RAY DIFFRACTION25chain 'D' and (resid 85 through 103 )D85 - 103
26X-RAY DIFFRACTION26chain 'D' and (resid 104 through 108 )D104 - 108
27X-RAY DIFFRACTION27chain 'E' and (resid 1 through 18 )E1 - 18
28X-RAY DIFFRACTION28chain 'E' and (resid 19 through 25 )E19 - 25
29X-RAY DIFFRACTION29chain 'E' and (resid 26 through 38 )E26 - 38
30X-RAY DIFFRACTION30chain 'E' and (resid 39 through 48 )E39 - 48
31X-RAY DIFFRACTION31chain 'E' and (resid 49 through 61 )E49 - 61
32X-RAY DIFFRACTION32chain 'E' and (resid 62 through 84 )E62 - 84
33X-RAY DIFFRACTION33chain 'E' and (resid 85 through 90 )E85 - 90
34X-RAY DIFFRACTION34chain 'E' and (resid 91 through 103 )E91 - 103
35X-RAY DIFFRACTION35chain 'E' and (resid 104 through 108 )E104 - 108
36X-RAY DIFFRACTION36chain 'F' and (resid 1 through 7 )F1 - 7
37X-RAY DIFFRACTION37chain 'F' and (resid 8 through 18 )F8 - 18
38X-RAY DIFFRACTION38chain 'F' and (resid 19 through 25 )F19 - 25
39X-RAY DIFFRACTION39chain 'F' and (resid 26 through 32 )F26 - 32
40X-RAY DIFFRACTION40chain 'F' and (resid 33 through 48 )F33 - 48
41X-RAY DIFFRACTION41chain 'F' and (resid 49 through 61 )F49 - 61
42X-RAY DIFFRACTION42chain 'F' and (resid 62 through 67 )F62 - 67
43X-RAY DIFFRACTION43chain 'F' and (resid 68 through 75 )F68 - 75
44X-RAY DIFFRACTION44chain 'F' and (resid 76 through 84 )F76 - 84
45X-RAY DIFFRACTION45chain 'F' and (resid 85 through 90 )F85 - 90
46X-RAY DIFFRACTION46chain 'F' and (resid 91 through 103 )F91 - 103
47X-RAY DIFFRACTION47chain 'F' and (resid 104 through 108 )F104 - 108
48X-RAY DIFFRACTION48chain 'G' and (resid 1 through 17 )G1 - 17
49X-RAY DIFFRACTION49chain 'G' and (resid 18 through 25 )G18 - 25
50X-RAY DIFFRACTION50chain 'G' and (resid 26 through 39 )G26 - 39
51X-RAY DIFFRACTION51chain 'G' and (resid 40 through 51 )G40 - 51
52X-RAY DIFFRACTION52chain 'G' and (resid 52 through 60 )G52 - 60
53X-RAY DIFFRACTION53chain 'G' and (resid 61 through 83 )G61 - 83
54X-RAY DIFFRACTION54chain 'G' and (resid 84 through 99 )G84 - 99
55X-RAY DIFFRACTION55chain 'G' and (resid 100 through 119 )G100 - 119
56X-RAY DIFFRACTION56chain 'G' and (resid 120 through 126 )G120 - 126
57X-RAY DIFFRACTION57chain 'H' and (resid 1 through 39 )H1 - 39
58X-RAY DIFFRACTION58chain 'H' and (resid 40 through 51 )H40 - 51
59X-RAY DIFFRACTION59chain 'H' and (resid 52 through 60 )H52 - 60
60X-RAY DIFFRACTION60chain 'H' and (resid 61 through 83 )H61 - 83
61X-RAY DIFFRACTION61chain 'H' and (resid 84 through 99 )H84 - 99
62X-RAY DIFFRACTION62chain 'H' and (resid 100 through 109 )H100 - 109
63X-RAY DIFFRACTION63chain 'H' and (resid 110 through 119 )H110 - 119
64X-RAY DIFFRACTION64chain 'H' and (resid 120 through 126 )H120 - 126
65X-RAY DIFFRACTION65chain 'I' and (resid 1 through 39 )I1 - 39
66X-RAY DIFFRACTION66chain 'I' and (resid 40 through 51 )I40 - 51
67X-RAY DIFFRACTION67chain 'I' and (resid 52 through 60 )I52 - 60
68X-RAY DIFFRACTION68chain 'I' and (resid 61 through 73 )I61 - 73
69X-RAY DIFFRACTION69chain 'I' and (resid 74 through 83 )I74 - 83
70X-RAY DIFFRACTION70chain 'I' and (resid 84 through 99 )I84 - 99
71X-RAY DIFFRACTION71chain 'I' and (resid 100 through 109 )I100 - 109
72X-RAY DIFFRACTION72chain 'I' and (resid 110 through 125 )I110 - 125
73X-RAY DIFFRACTION73chain 'J' and (resid 6 through 22 )J6 - 22
74X-RAY DIFFRACTION74chain 'J' and (resid 23 through 44 )J23 - 44
75X-RAY DIFFRACTION75chain 'J' and (resid 45 through 67 )J45 - 67
76X-RAY DIFFRACTION76chain 'J' and (resid 68 through 75 )J68 - 75
77X-RAY DIFFRACTION77chain 'J' and (resid 76 through 98 )J76 - 98
78X-RAY DIFFRACTION78chain 'J' and (resid 99 through 112 )J99 - 112
79X-RAY DIFFRACTION79chain 'J' and (resid 113 through 126 )J113 - 126
80X-RAY DIFFRACTION80chain 'J' and (resid 127 through 136 )J127 - 136
81X-RAY DIFFRACTION81chain 'J' and (resid 137 through 158 )J137 - 158
82X-RAY DIFFRACTION82chain 'K' and (resid 6 through 22 )K6 - 22
83X-RAY DIFFRACTION83chain 'K' and (resid 23 through 32 )K23 - 32
84X-RAY DIFFRACTION84chain 'K' and (resid 33 through 53 )K33 - 53
85X-RAY DIFFRACTION85chain 'K' and (resid 54 through 67 )K54 - 67
86X-RAY DIFFRACTION86chain 'K' and (resid 68 through 75 )K68 - 75
87X-RAY DIFFRACTION87chain 'K' and (resid 76 through 98 )K76 - 98
88X-RAY DIFFRACTION88chain 'K' and (resid 99 through 112 )K99 - 112
89X-RAY DIFFRACTION89chain 'K' and (resid 113 through 126 )K113 - 126
90X-RAY DIFFRACTION90chain 'K' and (resid 127 through 150 )K127 - 150
91X-RAY DIFFRACTION91chain 'K' and (resid 151 through 158 )K151 - 158
92X-RAY DIFFRACTION92chain 'L' and (resid 6 through 32 )L6 - 32
93X-RAY DIFFRACTION93chain 'L' and (resid 33 through 53 )L33 - 53
94X-RAY DIFFRACTION94chain 'L' and (resid 54 through 126 )L54 - 126
95X-RAY DIFFRACTION95chain 'L' and (resid 127 through 158 )L127 - 158
96X-RAY DIFFRACTION96chain 'M' and (resid 1 through 7 )M1 - 7
97X-RAY DIFFRACTION97chain 'M' and (resid 8 through 18 )M8 - 18
98X-RAY DIFFRACTION98chain 'M' and (resid 19 through 25 )M19 - 25
99X-RAY DIFFRACTION99chain 'M' and (resid 26 through 38 )M26 - 38
100X-RAY DIFFRACTION100chain 'M' and (resid 39 through 48 )M39 - 48
101X-RAY DIFFRACTION101chain 'M' and (resid 49 through 67 )M49 - 67
102X-RAY DIFFRACTION102chain 'M' and (resid 68 through 84 )M68 - 84
103X-RAY DIFFRACTION103chain 'M' and (resid 85 through 103 )M85 - 103
104X-RAY DIFFRACTION104chain 'M' and (resid 104 through 108 )M104 - 108
105X-RAY DIFFRACTION105chain 'N' and (resid 1 through 7 )N1 - 7
106X-RAY DIFFRACTION106chain 'N' and (resid 8 through 25 )N8 - 25
107X-RAY DIFFRACTION107chain 'N' and (resid 26 through 38 )N26 - 38
108X-RAY DIFFRACTION108chain 'N' and (resid 39 through 48 )N39 - 48
109X-RAY DIFFRACTION109chain 'N' and (resid 49 through 61 )N49 - 61
110X-RAY DIFFRACTION110chain 'N' and (resid 62 through 75 )N62 - 75
111X-RAY DIFFRACTION111chain 'N' and (resid 76 through 90 )N76 - 90
112X-RAY DIFFRACTION112chain 'N' and (resid 91 through 103 )N91 - 103
113X-RAY DIFFRACTION113chain 'N' and (resid 104 through 108 )N104 - 108
114X-RAY DIFFRACTION114chain 'O' and (resid 1 through 25 )O1 - 25
115X-RAY DIFFRACTION115chain 'O' and (resid 26 through 48 )O26 - 48
116X-RAY DIFFRACTION116chain 'O' and (resid 49 through 67 )O49 - 67
117X-RAY DIFFRACTION117chain 'O' and (resid 68 through 83 )O68 - 83
118X-RAY DIFFRACTION118chain 'O' and (resid 84 through 103 )O84 - 103
119X-RAY DIFFRACTION119chain 'O' and (resid 104 through 108 )O104 - 108
120X-RAY DIFFRACTION120chain 'P' and (resid 1 through 17 )P1 - 17
121X-RAY DIFFRACTION121chain 'P' and (resid 18 through 39 )P18 - 39
122X-RAY DIFFRACTION122chain 'P' and (resid 40 through 51 )P40 - 51
123X-RAY DIFFRACTION123chain 'P' and (resid 52 through 60 )P52 - 60
124X-RAY DIFFRACTION124chain 'P' and (resid 61 through 83 )P61 - 83
125X-RAY DIFFRACTION125chain 'P' and (resid 84 through 99 )P84 - 99
126X-RAY DIFFRACTION126chain 'P' and (resid 100 through 119 )P100 - 119
127X-RAY DIFFRACTION127chain 'P' and (resid 120 through 126 )P120 - 126
128X-RAY DIFFRACTION128chain 'Q' and (resid 1 through 39 )Q1 - 39
129X-RAY DIFFRACTION129chain 'Q' and (resid 40 through 51 )Q40 - 51
130X-RAY DIFFRACTION130chain 'Q' and (resid 52 through 60 )Q52 - 60
131X-RAY DIFFRACTION131chain 'Q' and (resid 61 through 83 )Q61 - 83
132X-RAY DIFFRACTION132chain 'Q' and (resid 84 through 99 )Q84 - 99
133X-RAY DIFFRACTION133chain 'Q' and (resid 100 through 119 )Q100 - 119
134X-RAY DIFFRACTION134chain 'Q' and (resid 120 through 126 )Q120 - 126
135X-RAY DIFFRACTION135chain 'R' and (resid 1 through 17 )R1 - 17
136X-RAY DIFFRACTION136chain 'R' and (resid 18 through 39 )R18 - 39
137X-RAY DIFFRACTION137chain 'R' and (resid 40 through 60 )R40 - 60
138X-RAY DIFFRACTION138chain 'R' and (resid 61 through 99 )R61 - 99
139X-RAY DIFFRACTION139chain 'R' and (resid 100 through 119 )R100 - 119
140X-RAY DIFFRACTION140chain 'R' and (resid 120 through 126 )R120 - 126

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万見について

-
お知らせ

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2022年2月9日: EMDBエントリの付随情報ファイルのフォーマットが新しくなりました

EMDBエントリの付随情報ファイルのフォーマットが新しくなりました

  • EMDBのヘッダファイルのバージョン3が、公式のフォーマットとなりました。
  • これまでは公式だったバージョン1.9は、アーカイブから削除されます。

関連情報:EMDBヘッダ

外部リンク:wwPDBはEMDBデータモデルのバージョン3へ移行します

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2020年8月12日: 新型コロナ情報

新型コロナ情報

URL: https://pdbj.org/emnavi/covid19.php

新ページ: EM Navigatorに新型コロナウイルスの特設ページを開設しました。

関連情報:Covid-19情報 / 2020年3月5日: 新型コロナウイルスの構造データ

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2020年3月5日: 新型コロナウイルスの構造データ

新型コロナウイルスの構造データ

関連情報:万見生物種 / 2020年8月12日: 新型コロナ情報

外部リンク:COVID-19特集ページ - PDBj / 今月の分子2020年2月：コロナウイルスプロテーアーゼ

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2019年1月31日: EMDBのIDの桁数の変更

EMDBのIDの桁数の変更

  • EMDBエントリに付与されているアクセスコード(EMDB-ID)は4桁の数字(例、EMD-1234)でしたが、間もなく枯渇します。これまでの4桁のID番号は4桁のまま変更されませんが、4桁の数字を使い切った後に発行されるIDは5桁以上の数字(例、EMD-12345)になります。5桁のIDは2019年の春頃から発行される見通しです。
  • EM Navigator/万見では、接頭語「EMD-」は省略されています。

関連情報:Q: 「EMD」とは何ですか？ / 万見/EM NavigatorにおけるID/アクセスコードの表記

外部リンク:EMDB Accession Codes are Changing Soon! / PDBjへお問い合わせ

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2017年7月12日: PDB大規模アップデート

PDB大規模アップデート

  • 新バージョンのPDBx/mmCIF辞書形式に基づくデータがリリースされました。
  • 今回の更新はバージョン番号が4から5になる大規模なもので、全エントリデータの書き換えが行われる「Remediation」というアップデートに該当します。
  • このバージョンアップで、電子顕微鏡の実験手法に関する多くの項目の書式が改定されました(例：em_softwareなど)。
  • EM NavigatorとYorodumiでも、この改定に基づいた表示内容になります。

外部リンク:wwPDB Remediation / OneDepデータ基準に準拠した、より強化された内容のモデル構造ファイルが、PDBアーカイブで公開されました。

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万見 (Yorodumi)

幾万の構造データを、幾万の視点から

  • 万見(Yorodumi)は、EMDB/PDB/SASBDBなどの構造データを閲覧するためのページです。
  • EM Navigatorの詳細ページの後継、Omokage検索のフロントエンドも兼ねています。

関連情報:EMDB / PDB / SASBDB / 3つのデータバンクの比較 / 万見検索 / 2016年8月31日: 新しいEM Navigatorと万見 / 万見文献 / Jmol/JSmol / 機能・相同性情報 / 新しいEM Navigatorと万見の変更点

他の情報も見る