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- PDB-5mu8: HUMAN TNF-ALPHA IN COMPLEX WITH JNJ525 -

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基本情報

登録情報
データベース: PDB / ID: 5mu8
タイトルHUMAN TNF-ALPHA IN COMPLEX WITH JNJ525
要素Tumor necrosis factor
キーワードCYTOKINE / TUMOR NECROSIS FACTOR ALPHA / PROTEROS BIOSTRUCTURES GMBH
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 / Sandwich / Mainly Beta
類似検索 - ドメイン・相同性
Chem-JNI / 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: 3 Å
データ登録者Blevitt, J.M. / Hack, M.D. / Herman, K.L. / Jackson, P.F. / Krawczuk, P.J. / Lebsack, A.D. / Liu, A.X. / Mirzadegan, T. / Nelen, M.I. / Patrick, A.P. ...Blevitt, J.M. / Hack, M.D. / Herman, K.L. / Jackson, P.F. / Krawczuk, P.J. / Lebsack, A.D. / Liu, A.X. / Mirzadegan, T. / Nelen, M.I. / Patrick, A.P. / Steinbacher, S. / Milla, M.E. / Lumb, K.J.
引用ジャーナル: J. Med. Chem. / 年: 2017
タイトル: Structural Basis of Small-Molecule Aggregate Induced Inhibition of a Protein-Protein Interaction.
著者: Blevitt, J.M. / Hack, M.D. / Herman, K.L. / Jackson, P.F. / Krawczuk, P.J. / Lebsack, A.D. / Liu, A.X. / Mirzadegan, T. / Nelen, M.I. / Patrick, A.N. / Steinbacher, S. / Milla, M.E. / Lumb, K.J.
履歴
登録2017年1月12日登録サイト: PDBE / 処理サイト: PDBE
改定 1.02017年3月29日Provider: repository / タイプ: Initial release
改定 1.12017年4月12日Group: Database references
改定 1.22017年5月10日Group: Database references
改定 1.32019年2月20日Group: Advisory / Data collection / Derived calculations
カテゴリ: diffrn_radiation_wavelength / pdbx_data_processing_status ...diffrn_radiation_wavelength / pdbx_data_processing_status / pdbx_validate_symm_contact / struct_conn / struct_conn_type
改定 1.42024年11月13日Group: Data collection / Database references / Structure summary
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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: Tumor necrosis factor
F: Tumor necrosis factor
G: Tumor necrosis factor
H: Tumor necrosis factor
I: Tumor necrosis factor
J: Tumor necrosis factor
K: Tumor necrosis factor
L: Tumor necrosis factor
M: Tumor necrosis factor
N: Tumor necrosis factor
O: Tumor necrosis factor
P: Tumor necrosis factor
Q: Tumor necrosis factor
R: Tumor necrosis factor
S: Tumor necrosis factor
T: Tumor necrosis factor
U: Tumor necrosis factor
V: Tumor necrosis factor
W: Tumor necrosis factor
X: Tumor necrosis factor
Y: Tumor necrosis factor
Z: Tumor necrosis factor
a: Tumor necrosis factor
b: Tumor necrosis factor
c: Tumor necrosis factor
d: Tumor necrosis factor
e: Tumor necrosis factor
f: Tumor necrosis factor
g: Tumor necrosis factor
h: Tumor necrosis factor
i: Tumor necrosis factor
j: Tumor necrosis factor
k: Tumor necrosis factor
l: Tumor necrosis factor
m: Tumor necrosis factor
n: Tumor necrosis factor
o: Tumor necrosis factor
p: Tumor necrosis factor
q: Tumor necrosis factor
r: Tumor necrosis factor
s: Tumor necrosis factor
t: Tumor necrosis factor
u: Tumor necrosis factor
v: Tumor necrosis factor
w: Tumor necrosis factor
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)867,17394
ポリマ－843,50148
非ポリマー23,67346
水00
1
A: Tumor necrosis factor
B: Tumor necrosis factor
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)36,1754
ポリマ－35,1462
非ポリマー1,0292
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area2370 Å2
ΔGint-13 kcal/mol
Surface area14300 Å2
手法PISA
2
C: Tumor necrosis factor
D: Tumor necrosis factor
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)36,6905
ポリマ－35,1462
非ポリマー1,5443
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area2880 Å2
ΔGint-12 kcal/mol
Surface area14980 Å2
手法PISA
3
F: Tumor necrosis factor
G: Tumor necrosis factor
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)36,1754
ポリマ－35,1462
非ポリマー1,0292
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area2390 Å2
ΔGint-11 kcal/mol
Surface area14750 Å2
手法PISA
4
H: Tumor necrosis factor
I: Tumor necrosis factor
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)36,1754
ポリマ－35,1462
非ポリマー1,0292
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area2410 Å2
ΔGint-14 kcal/mol
Surface area14560 Å2
手法PISA
5
J: Tumor necrosis factor
K: Tumor necrosis factor
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)36,1754
ポリマ－35,1462
非ポリマー1,0292
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area2550 Å2
ΔGint-11 kcal/mol
Surface area14400 Å2
手法PISA
6
L: Tumor necrosis factor
M: Tumor necrosis factor
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)36,1754
ポリマ－35,1462
非ポリマー1,0292
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area2760 Å2
ΔGint-16 kcal/mol
Surface area14800 Å2
手法PISA
7
N: Tumor necrosis factor
O: Tumor necrosis factor
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)35,6603
ポリマ－35,1462
非ポリマー5151
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area2390 Å2
ΔGint-10 kcal/mol
Surface area14410 Å2
手法PISA
8
P: Tumor necrosis factor
Q: Tumor necrosis factor
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)36,6905
ポリマ－35,1462
非ポリマー1,5443
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area2920 Å2
ΔGint-12 kcal/mol
Surface area15290 Å2
手法PISA
9
R: Tumor necrosis factor
S: Tumor necrosis factor
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)35,6603
ポリマ－35,1462
非ポリマー5151
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area2380 Å2
ΔGint-9 kcal/mol
Surface area14140 Å2
手法PISA
10
T: Tumor necrosis factor
U: Tumor necrosis factor
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)35,6603
ポリマ－35,1462
非ポリマー5151
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area2630 Å2
ΔGint-13 kcal/mol
Surface area14800 Å2
手法PISA
11
V: Tumor necrosis factor
W: Tumor necrosis factor
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)36,1754
ポリマ－35,1462
非ポリマー1,0292
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area2530 Å2
ΔGint-9 kcal/mol
Surface area13980 Å2
手法PISA
12
X: Tumor necrosis factor
Y: Tumor necrosis factor
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)36,1754
ポリマ－35,1462
非ポリマー1,0292
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area2740 Å2
ΔGint-13 kcal/mol
Surface area14910 Å2
手法PISA
13
Z: Tumor necrosis factor
a: Tumor necrosis factor
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)36,1754
ポリマ－35,1462
非ポリマー1,0292
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area2360 Å2
ΔGint-11 kcal/mol
Surface area14810 Å2
手法PISA
14
b: Tumor necrosis factor
c: Tumor necrosis factor
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)36,1754
ポリマ－35,1462
非ポリマー1,0292
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area2600 Å2
ΔGint-14 kcal/mol
Surface area14770 Å2
手法PISA
15
d: Tumor necrosis factor
e: Tumor necrosis factor
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)35,6603
ポリマ－35,1462
非ポリマー5151
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area2550 Å2
ΔGint-9 kcal/mol
Surface area14210 Å2
手法PISA
16
f: Tumor necrosis factor
g: Tumor necrosis factor
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)36,1754
ポリマ－35,1462
非ポリマー1,0292
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area1980 Å2
ΔGint-11 kcal/mol
Surface area14970 Å2
手法PISA
17
h: Tumor necrosis factor
i: Tumor necrosis factor
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)36,1754
ポリマ－35,1462
非ポリマー1,0292
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area2390 Å2
ΔGint-11 kcal/mol
Surface area14420 Å2
手法PISA
18
j: Tumor necrosis factor
k: Tumor necrosis factor
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)36,1754
ポリマ－35,1462
非ポリマー1,0292
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area2630 Å2
ΔGint-12 kcal/mol
Surface area14680 Å2
手法PISA
19
l: Tumor necrosis factor
m: Tumor necrosis factor
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)35,6603
ポリマ－35,1462
非ポリマー5151
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area2280 Å2
ΔGint-9 kcal/mol
Surface area14530 Å2
手法PISA
20
n: Tumor necrosis factor
o: Tumor necrosis factor
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)36,6905
ポリマ－35,1462
非ポリマー1,5443
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area3050 Å2
ΔGint-12 kcal/mol
Surface area15090 Å2
手法PISA
21
p: Tumor necrosis factor
q: Tumor necrosis factor
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)36,1754
ポリマ－35,1462
非ポリマー1,0292
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area2600 Å2
ΔGint-13 kcal/mol
Surface area14650 Å2
手法PISA
22
r: Tumor necrosis factor
s: Tumor necrosis factor
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)36,1754
ポリマ－35,1462
非ポリマー1,0292
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area2520 Å2
ΔGint-12 kcal/mol
Surface area14640 Å2
手法PISA
23
t: Tumor necrosis factor
u: Tumor necrosis factor
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)36,1754
ポリマ－35,1462
非ポリマー1,0292
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area2500 Å2
ΔGint-10 kcal/mol
Surface area14710 Å2
手法PISA
24
v: Tumor necrosis factor
w: Tumor necrosis factor
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)36,1754
ポリマ－35,1462
非ポリマー1,0292
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area2540 Å2
ΔGint-12 kcal/mol
Surface area14670 Å2
手法PISA
単位格子
Length a, b, c (Å)104.888, 118.348, 186.747
Angle α, β, γ (deg.)97.57, 94.31, 98.75
Int Tables number1
Space group name H-MP1

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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: 17572.932 Da / 分子数: 48 / 断片: UNP residues 77-233 / 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: Escherichia coli (大腸菌) / 参照: UniProt: P01375
#2: 化合物...
ChemComp-JNI / ~{N}4-(phenylmethyl)-~{N}4-[2-[3-(2-piperazin-1-ylpyrimidin-5-yl)phenyl]phenyl]pyrimidine-2,4-diamine


分子量: 514.624 Da / 分子数: 46 / 由来タイプ: 合成 / 式: C31H30N8
Has protein modificationY

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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: 2.81 Å3/Da / 溶媒含有率: 56.25 %
結晶化温度: 293 K / 手法: 蒸気拡散法, シッティングドロップ法 / 詳細: PEG

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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: NSLS / ビームライン: X6A / 波長: 1 Å
検出器タイプ: DECTRIS PILATUS3 S 6M / 検出器: PIXEL / 日付: 2015年8月17日
詳細: Si (111) monochromator followed by a toroidal focusing mirror
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: 3→184.24 Å / Num. obs: 158847 / % possible obs: 90.6 % / Observed criterion σ(I): 0 / 冗長度: 1.9 % / Rmerge(I) obs: 0.068 / Net I/σ(I): 7.58
反射 シェル解像度: 3→3.25 Å / 冗長度: 1.9 % / Rmerge(I) obs: 0.677 / % possible all: 90.4

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解析

ソフトウェア
名称バージョン分類
XDSデータ削減
XSCALEデータスケーリング
REFMAC5.8.0049精密化
精密化構造決定の手法: 分子置換 / 解像度: 3→184.24 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.906 / SU B: 69.685 / SU ML: 0.573 / 交差検証法: THROUGHOUT / ESU R Free: 0.555 / 詳細: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor反射数%反射Selection details
Rfree0.3 445 0.3 %RANDOM
Rwork0.21107 ---
obs0.21131 158401 90.6 %-
溶媒の処理イオンプローブ半径: 0.8 Å / 減衰半径: 0.8 Å / VDWプローブ半径: 1.2 Å
原子変位パラメータBiso mean: 114.51 Å2
Baniso -1Baniso -2Baniso -3
1--3.07 Å22.12 Å2-0.66 Å2
2--4.15 Å2-1.03 Å2
3----1.38 Å2
精密化ステップサイクル: LAST / 解像度: 3→184.24 Å
タンパク質核酸リガンド溶媒全体
原子数54511 0 1794 0 56305
拘束条件
Refine-IDタイプDev idealDev ideal target数
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01957790
X-RAY DIFFRACTIONr_bond_other_d0.0010.0254951
X-RAY DIFFRACTIONr_angle_refined_deg1.4482.00678695
X-RAY DIFFRACTIONr_angle_other_deg2.4133125964
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.64456866
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.87524.5352540
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.413159089
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.215310
X-RAY DIFFRACTIONr_chiral_restr0.0790.28516
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02165580
X-RAY DIFFRACTIONr_gen_planes_other0.0030.0213606
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it5.1754.55827731
X-RAY DIFFRACTIONr_mcbond_other5.1754.55827730
X-RAY DIFFRACTIONr_mcangle_it8.1757.65334508
X-RAY DIFFRACTIONr_mcangle_other8.1757.65334509
X-RAY DIFFRACTIONr_scbond_it7.7985.86230059
X-RAY DIFFRACTIONr_scbond_other7.7985.86230059
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other11.3859.57244187
X-RAY DIFFRACTIONr_long_range_B_refined15.10323.81761250
X-RAY DIFFRACTIONr_long_range_B_other15.10323.81761251
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS精密化 シェル解像度: 3→3.078 Å / Total num. of bins used: 20
Rfactor反射数%反射
Rfree0.415 33 -
Rwork0.346 11123 -
obs--85.88 %
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)
15.53340.7153-0.81693.5637-0.25756.6094-0.0910.68190.1862-0.52810.07990.4596-0.1422-0.40390.01120.76880.0162-0.30090.2288-0.051.218525.47520.68211.122
24.1914-0.4069-1.59033.6848-0.15096.41010.03010.01830.4527-0.104-0.03560.1589-0.21270.05680.00550.5778-0.049-0.20330.0473-0.16620.941343.73419.16121.857
34.1605-0.4427-1.01242.7883-0.72237.116-0.1928-0.2320.17310.16150.11120.6697-0.3111-1.28370.08170.8793-0.0522-0.06530.455-0.16711.423615.277-6.2529.245
43.38320.6965-0.59762.9764-0.71326.6432-0.2063-0.332-0.280.11930.07220.28580.2818-0.27360.1340.64430.011-0.08010.0825-0.11460.907136.626-10.69729.847
57.25790.2611-2.16253.9732-0.36346.852-0.13270.64390.104-0.4552-0.04270.1855-0.0346-0.19830.17540.62080.0109-0.18410.1739-0.05080.812167.5375.79899.496
64.5876-0.3836-1.24623.01050.19015.0018-0.02160.06930.36760.2222-0.048-0.0845-0.278-0.03360.06960.6678-0.0628-0.13470.0726-0.20530.817185.3295.561110.715
73.1439-0.4659-0.50932.3007-0.53916.4551-0.1457-0.3522-0.00440.41720.14580.5735-0.5925-1.2011-0.00011.1245-0.1262-0.00020.4742-0.12151.254957.746-20.604119.456
83.83070.9039-2.09452.5474-1.03526.0708-0.0104-0.2801-0.31610.2692-0.0650.12020.3516-0.15950.07550.8828-0.1455-0.1020.1334-0.15340.801979.502-24.201119.146
93.8942-0.74750.58242.94-1.30656.6835-0.0931-0.64110.00120.4792-0.02560.5632-0.4001-1.2660.11870.9649-0.01710.06940.699-0.09521.2304-2.2633.26132.584
102.86790.2650.11972.5594-0.36517.5890.0254-0.3279-0.27390.2573-0.02230.17540.2716-0.2466-0.00320.7397-0.0182-0.04060.0801-0.1340.8218.30832.117128.239
115.3230.4104-2.50622.31040.83559.0933-0.07550.5195-0.2547-0.068-0.03470.63270.0938-1.57250.11021.15560.2929-0.13290.7389-0.02391.2696-3.30159.261111.437
123.2424-0.02190.02272.5401-0.55647.0411-0.03040.14610.2176-0.05580.02740.226-0.7017-0.2970.00290.90240.0276-0.08550.0565-0.1580.801518.14561.946115.999
138.33950.2388-1.26432.9564-0.18954.7995-0.0181-0.1519-0.19050.18620.04670.006-0.09180.0324-0.02861.0758-0.0267-0.12360.1362-0.24720.605543.0864.381159.334
146.073-0.5052-0.71623.11780.77074.1611-0.00040.06240.1396-0.05060.07330.0426-0.4550.0662-0.07291.0317-0.1045-0.090.088-0.17680.596539.63264.144138.458
156.81730.2341-2.13222.37920.99775.5457-0.0234-0.47440.00020.39220.1004-0.67150.08750.9633-0.07691.31440.1485-0.23660.6485-0.14990.944861.91135.948153.764
165.589-1.4043-2.07392.83730.8834.6417-0.0624-0.1138-0.40190.19170.1975-0.13310.33190.5682-0.13521.02460.02-0.20170.1544-0.25360.742247.64833.388137.036
173.6455-0.02140.61953.13890.59446.04840.01-0.1297-0.32160.25130.18-0.59280.41121.1024-0.190.8178-0.0448-0.11740.3766-0.22541.057829.463-1.423102.212
185.12080.98772.23563.54480.81694.75860.0593-0.3560.20310.41-0.1147-0.19210.01720.24870.05530.7499-0.0242-0.12140.0956-0.1450.753211.1112.243112.168
197.5576-0.00390.9433.673-0.65757.3811-0.18210.59820.0049-0.20530.1069-0.43090.37410.38440.07511.00570.037-0.0570.1466-0.26320.8313.943-28.35488.654
205.2305-0.10290.85613.07090.5184.8768-0.0359-0.1576-0.32910.1528-0.0728-0.04220.91740.04130.10861.04790.0558-0.05020.0839-0.07280.77561.53-27.935106.509
214.35510.0445-0.62972.89331.18946.23430.03950.12930.1369-0.15840.0433-0.86850.25611.3425-0.08290.937-0.08740.02330.3989-0.1321.325592.02310.0369.923
224.37440.2141.97933.11330.20416.4986-0.0049-0.11680.5052-0.0875-0.133-0.18930.05180.39570.13780.70630.0044-0.0280.0597-0.11530.811673.81313.87120.366
236.9577-0.69672.26323.088-1.30047.2302-0.07360.67130.3888-0.3492-0.0513-0.1128-0.07870.25740.12491.1504-0.0248-0.01390.1737-0.24220.744873.31-14.805-4.931
246.37290.161.87092.6397-0.1574.8132-0.08730.2148-0.269-0.18090.00380.09590.4651-0.21710.08340.91320.028-0.00510.0485-0.12790.642162.566-14.86213.889
254.9443-0.1161.70652.1033-0.04637.3966-0.0368-0.6716-0.06370.55640.03580.546-0.1983-0.84850.00090.9491-0.0524-0.03070.350.0011.281361.05445.34838.006
263.11990.2105-0.83722.98990.08096.2028-0.0044-0.4075-0.48370.36040.0047-0.06720.29160.1136-0.00040.7879-0.0286-0.2110.0888-0.10681.081581.92745.04134.361
275.42380.4294-1.5972.89130.36749.1638-0.050.348-0.0628-0.38220.03350.37620.1608-1.00570.01660.88560.1307-0.170.2475-0.07071.142660.51272.31817.214
283.7747-0.0586-0.64033.2435-0.20016.5440.04960.0340.2219-0.1078-0.02960.1286-0.4242-0.0678-0.01990.75760.0038-0.12270.0385-0.17640.881581.06875.06324.233
295.81380.29710.34484.157-0.15385.09850.16140.86350.4806-0.6379-0.0283-0.174-0.21510.1705-0.1331.17310.03560.02010.392-0.24910.857147.49129.74687.154
305.72620.53181.41893.03381.02874.42750.13420.1165-0.03050.05110.06130.05770.25420.2377-0.19540.81740.04-0.08140.0452-0.16050.719440.81630.67107.231
315.22610.31531.56113.14771.17116.45740.08540.8749-0.0379-0.4649-0.0726-0.64590.33951.3787-0.01281.3912-0.17490.18670.8797-0.15061.162463.6559.09693.892
326.19551.31112.82693.74451.02935.7904-0.02840.10540.3769-0.19760.0953-0.1756-0.50890.7111-0.06690.9543-0.18020.05170.1761-0.19180.717147.75961.575108.972
336.641-1.57550.11873.8372-0.97425.211-0.1568-0.9268-0.23170.7240.14860.236-0.13-0.32220.00811.3340.0055-0.13360.4816-0.33990.764860.87214.65568.977
345.8286-1.4896-0.93883.19370.19893.98780.0267-0.29610.37270.2695-0.10730.1264-0.2773-0.10640.08060.8866-0.0346-0.16250.1334-0.25230.705160.11315.78447.736
357.8771-0.4232-0.71553.55050.51534.8480.2399-1.0120.18260.491-0.1044-0.5578-0.2560.708-0.13551.2955-0.0128-0.18830.6271-0.06180.972874.26-16.28463.523
366.936-1.9792-0.71184.45330.4433.3295-0.0115-0.2385-0.36320.2871-0.0640.11170.2592-0.00680.07540.8579-0.0339-0.12160.1409-0.08880.605862.143-15.08245.144
376.64290.0243-1.24562.4639-0.63014.9751-0.0639-0.221-0.43050.50720.01860.10650.14590.03420.04541.0765-0.0458-0.10090.2541-0.28810.8425-1.33977.6368.567
385.9903-0.0965-1.47922.3566-0.05413.53370.2616-0.08710.16080.0355-0.13380.1093-0.2144-0.0372-0.12780.9247-0.1285-0.14710.2376-0.22460.7692-3.97577.57847.394
395.22650.897-2.37162.09791.11855.44070.109-0.6328-0.15470.41510.1638-0.47570.17590.9417-0.27271.41690.2707-0.33140.9865-0.04681.334619.06150.66562.606
407.3977-1.1508-2.75492.89820.10333.5346-0.0942-0.5251-0.46230.1780.1314-0.24820.54530.5673-0.03731.0090.0334-0.30470.3788-0.13310.97685.4747.32845.525
418.71420.13110.15332.3494-1.09664.7238-0.10111.5316-0.162-0.63080.1964-0.16170.04490.3723-0.09541.3704-0.1292-0.02550.7385-0.59811.27448.87345.285-4.354
426.31690.99631.56891.72060.04674.1094-0.01780.2144-0.460.00980.1248-0.10710.31660.1492-0.10690.92130.0672-0.130.113-0.28521.07880.745.23515.132
435.87230.09191.11833.36971.24425.82250.07870.922-0.1526-0.56810.0142-0.64960.18021.0667-0.0931.2978-0.06970.11070.8691-0.39611.275322.83175.1273.773
445.691.4752.64353.80451.07673.6740.05140.00690.1764-0.2938-0.0039-0.148-0.10740.3954-0.04760.9274-0.03340.00730.1509-0.28570.86046.52276.60418.422
458.6533-1.2195-1.07722.5107-0.66633.70970.0231-0.8021-0.32590.4870.07960.2925-0.1233-0.1674-0.10261.3469-0.1099-0.15420.5821-0.250.848-6.7024.595159.222
466.1093-0.3485-1.56352.49030.60883.55180.2009-0.08630.40410.1531-0.1569-0.0637-0.3564-0.1231-0.04411.0813-0.1481-0.18670.3088-0.17670.6719-5.0714.558138.068
475.18640.5779-3.28812.23591.99734.90320.2415-0.99010.34840.47270.0545-0.40230.04880.7709-0.2961.8950.1012-0.33741.0420.03071.20659.583-25.411157.171
487.6779-1.4455-2.42743.09650.38233.9675-0.0886-0.4765-0.59320.2517-0.0337-0.04950.70380.39470.12241.2115-0.0238-0.23830.3622-0.03230.7558-0.351-26.416137.478
精密化 TLSグループ
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A9 - 157
2X-RAY DIFFRACTION2B10 - 157
3X-RAY DIFFRACTION3C8 - 157
4X-RAY DIFFRACTION4D9 - 157
5X-RAY DIFFRACTION5F9 - 157
6X-RAY DIFFRACTION6G9 - 157
7X-RAY DIFFRACTION7H8 - 157
8X-RAY DIFFRACTION8I9 - 157
9X-RAY DIFFRACTION9J9 - 157
10X-RAY DIFFRACTION10K9 - 157
11X-RAY DIFFRACTION11L8 - 157
12X-RAY DIFFRACTION12M9 - 157
13X-RAY DIFFRACTION13N9 - 157
14X-RAY DIFFRACTION14O9 - 157
15X-RAY DIFFRACTION15P8 - 157
16X-RAY DIFFRACTION16Q9 - 157
17X-RAY DIFFRACTION17R9 - 157
18X-RAY DIFFRACTION18S9 - 157
19X-RAY DIFFRACTION19T8 - 157
20X-RAY DIFFRACTION20U9 - 157
21X-RAY DIFFRACTION21V9 - 157
22X-RAY DIFFRACTION22W9 - 157
23X-RAY DIFFRACTION23X8 - 157
24X-RAY DIFFRACTION24Y9 - 157
25X-RAY DIFFRACTION25Z9 - 157
26X-RAY DIFFRACTION26a9 - 157
27X-RAY DIFFRACTION27b8 - 157
28X-RAY DIFFRACTION28c9 - 157
29X-RAY DIFFRACTION29d9 - 157
30X-RAY DIFFRACTION30e9 - 157
31X-RAY DIFFRACTION31f8 - 157
32X-RAY DIFFRACTION32g9 - 157
33X-RAY DIFFRACTION33h9 - 157
34X-RAY DIFFRACTION34i9 - 157
35X-RAY DIFFRACTION35j8 - 157
36X-RAY DIFFRACTION36k9 - 157
37X-RAY DIFFRACTION37l9 - 157
38X-RAY DIFFRACTION38m9 - 157
39X-RAY DIFFRACTION39n8 - 157
40X-RAY DIFFRACTION40o9 - 157
41X-RAY DIFFRACTION41p9 - 157
42X-RAY DIFFRACTION42q9 - 157
43X-RAY DIFFRACTION43r8 - 157
44X-RAY DIFFRACTION44s9 - 157
45X-RAY DIFFRACTION45t9 - 157
46X-RAY DIFFRACTION46u9 - 157
47X-RAY DIFFRACTION47v8 - 157
48X-RAY DIFFRACTION48w9 - 157

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万見について

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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