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- PDB-7doc: Crystal structure of Zika NS2B-NS3 protease with compound 5 -

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基本情報

登録情報
データベース: PDB / ID: 7doc
タイトルCrystal structure of Zika NS2B-NS3 protease with compound 5
要素
  • (Core protein) x 4
  • (Genome polyprotein) x 2
  • 3-PYRIDIN-4-YL-2,4-DIHYDRO-INDENO[1,2-.C.]PYRAZOLE
  • Serine protease subunit NS2B
キーワードVIRAL PROTEIN / Viral protease / Protease inhibitor complex
機能・相同性
機能・相同性情報


symbiont-mediated suppression of host interferon-mediated signaling pathway / : / flavivirin / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity / ribonucleoside triphosphate phosphatase activity / viral capsid / double-stranded RNA binding / nucleoside-triphosphate phosphatase ...symbiont-mediated suppression of host interferon-mediated signaling pathway / : / flavivirin / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity / ribonucleoside triphosphate phosphatase activity / viral capsid / double-stranded RNA binding / nucleoside-triphosphate phosphatase / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / symbiont-mediated suppression of host toll-like receptor signaling pathway / protein-macromolecule adaptor activity / mRNA (guanine-N7)-methyltransferase / methyltransferase cap1 / clathrin-dependent endocytosis of virus by host cell / methyltransferase cap1 activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / host cell cytoplasm / RNA helicase activity / protein dimerization activity / host cell perinuclear region of cytoplasm / host cell endoplasmic reticulum membrane / RNA helicase / symbiont-mediated suppression of host innate immune response / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / symbiont entry into host cell / symbiont-mediated activation of host autophagy / RNA-directed RNA polymerase / serine-type endopeptidase activity / viral RNA genome replication / RNA-directed RNA polymerase activity / fusion of virus membrane with host endosome membrane / lipid binding / viral envelope / GTP binding / virion attachment to host cell / host cell nucleus / virion membrane / structural molecule activity / ATP hydrolysis activity / proteolysis / extracellular region / ATP binding / metal ion binding / membrane
類似検索 - 分子機能
Flavivirus non-structural protein NS2B / Flavivirus capsid protein C superfamily / Genome polyprotein, Flavivirus / : / Flavivirus non-structural protein NS4A / Flavivirus non-structural protein NS2B / Flavivirus non-structural protein NS4B / mRNA cap 0/1 methyltransferase / Flavivirus non-structural protein NS4B / Flavivirus non-structural protein NS4A ...Flavivirus non-structural protein NS2B / Flavivirus capsid protein C superfamily / Genome polyprotein, Flavivirus / : / Flavivirus non-structural protein NS4A / Flavivirus non-structural protein NS2B / Flavivirus non-structural protein NS4B / mRNA cap 0/1 methyltransferase / Flavivirus non-structural protein NS4B / Flavivirus non-structural protein NS4A / Flavivirus NS2B domain profile. / mRNA cap 0 and cap 1 methyltransferase (EC 2.1.1.56 and EC 2.1.1.57) domain profile. / Flavivirus non-structural protein NS2A / Flavivirus non-structural protein NS2A / Flavivirus NS3, petidase S7 / Peptidase S7, Flavivirus NS3 serine protease / Flavivirus NS3 protease (NS3pro) domain profile. / RNA-directed RNA polymerase, thumb domain, Flavivirus / Flavivirus RNA-directed RNA polymerase, thumb domain / RNA-directed RNA polymerase, flavivirus / Flavivirus RNA-directed RNA polymerase, fingers and palm domains / Flavivirus capsid protein C / Flavivirus capsid protein C / Flavivirus non-structural Protein NS1 / Flavivirus non-structural protein NS1 / Envelope glycoprotein M, flavivirus / Envelope glycoprotein M superfamily, flavivirus / Flavivirus envelope glycoprotein M / Flavivirus polyprotein propeptide / Flavivirus polyprotein propeptide superfamily / Flavivirus polyprotein propeptide / Flavivirus envelope glycoprotein E, stem/anchor domain / : / Flavivirus NS3 helicase, C-terminal helical domain / Flavivirus envelope glycoprotein E, Stem/Anchor domain / Flavivirus envelope glycoprotein E, Stem/Anchor domain superfamily / Flavivirus glycoprotein E, immunoglobulin-like domain / Flavivirus glycoprotein, immunoglobulin-like domain / Flavivirus glycoprotein central and dimerisation domain / Flavivirus glycoprotein, central and dimerisation domains / Flaviviral glycoprotein E, central domain, subdomain 1 / Flaviviral glycoprotein E, central domain, subdomain 2 / Ribosomal RNA methyltransferase, FtsJ domain / FtsJ-like methyltransferase / Flavivirus/Alphavirus glycoprotein, immunoglobulin-like domain superfamily / Flavivirus glycoprotein, central and dimerisation domain superfamily / Flaviviral glycoprotein E, dimerisation domain / DEAD box, Flavivirus / Flavivirus DEAD domain / helicase superfamily c-terminal domain / Immunoglobulin E-set / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / P-loop containing nucleoside triphosphate hydrolase
類似検索 - ドメイン・相同性
Genome polyprotein / Genome polyprotein / Genome polyprotein / Genome polyprotein
類似検索 - 構成要素
生物種Zika virus (ジカ熱ウイルス)
synthetic construct (人工物)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 1.904 Å
データ登録者Quek, J.P.
資金援助 シンガポール, 3件
組織認可番号国
Other governmentStart up grant シンガポール
Other governmentCBRG15May045 シンガポール
Other governmentNRF2016NRF-CRP001-063 シンガポール
引用ジャーナル: Acs Med.Chem.Lett. / 年: 2021
タイトル: 2-Cyanoisonicotinamide Conjugation: A Facile Approach to Generate Potent Peptide Inhibitors of the Zika Virus Protease.
著者: Patil, N.A. / Quek, J.P. / Schroeder, B. / Morewood, R. / Rademann, J. / Luo, D. / Nitsche, C.
履歴
登録2020年12月14日登録サイト: PDBJ / 処理サイト: PDBJ
改定 1.02021年4月14日Provider: repository / タイプ: Initial release
改定 1.12021年6月16日Group: Database references / カテゴリ: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation_author.identifier_ORCID
改定 2.02023年11月15日Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
カテゴリ: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.ptnr1_label_atom_id
改定 2.12023年11月29日Group: Refinement description / カテゴリ: pdbx_initial_refinement_model
改定 3.02024年7月10日Group: Data collection / Derived calculations ...Data collection / Derived calculations / Non-polymer description / Structure summary
カテゴリ: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / entity / struct_conn
Item: _chem_comp.formula / _chem_comp.formula_weight ..._chem_comp.formula / _chem_comp.formula_weight / _entity.formula_weight / _struct_conn.pdbx_leaving_atom_flag

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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: Core protein
B: Core protein
C: Genome polyprotein
D: Core protein
E: Serine protease subunit NS2B
F: Core protein
G: Core protein
H: Genome polyprotein
I: 3-PYRIDIN-4-YL-2,4-DIHYDRO-INDENO[1,2-.C.]PYRAZOLE


分子量 (理論値)分子数
合計 (水以外)83,9579
ポリマ－83,9579
非ポリマー00
水6,684371
1
A: Core protein
B: Core protein


分子量 (理論値)分子数
合計 (水以外)20,6902
ポリマ－20,6902
非ポリマー00
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area3780 Å2
ΔGint-26 kcal/mol
Surface area8850 Å2
手法PISA
2
C: Genome polyprotein
D: Core protein


分子量 (理論値)分子数
合計 (水以外)20,4322
ポリマ－20,4322
非ポリマー00
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area3780 Å2
ΔGint-28 kcal/mol
Surface area8390 Å2
手法PISA
3
E: Serine protease subunit NS2B
F: Core protein


分子量 (理論値)分子数
合計 (水以外)21,3062
ポリマ－21,3062
非ポリマー00
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area3700 Å2
ΔGint-26 kcal/mol
Surface area9150 Å2
手法PISA
4
G: Core protein
H: Genome polyprotein


分子量 (理論値)分子数
合計 (水以外)20,7182
ポリマ－20,7182
非ポリマー00
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area3810 Å2
ΔGint-27 kcal/mol
Surface area8930 Å2
手法PISA
5
I: 3-PYRIDIN-4-YL-2,4-DIHYDRO-INDENO[1,2-.C.]PYRAZOLE


  • 登録者・ソフトウェアが定義した集合体
  • 810 Da, 1 ポリマー
分子量 (理論値)分子数
合計 (水以外)8101
ポリマ－8101
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area1150 Å2
手法PISA
単位格子
Length a, b, c (Å)59.154, 59.614, 215.073
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID詳細
11(chain A and (resid 51 through 61 or (resid 62...
21(chain C and (resid 51 through 65 or (resid 66...
31(chain E and (resid 51 through 61 or (resid 62...
41(chain G and (resid 51 through 61 or (resid 62...
12(chain B and (resid 18 through 29 or (resid 30...
22(chain D and (resid 18 through 30 or resid 34...
32(chain F and (resid 18 through 60 or (resid 64...
42(chain H and (resid 18 through 30 or resid 34...

NCSドメイン領域:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 51 through 61 or (resid 62...A51 - 61
121(chain A and (resid 51 through 61 or (resid 62...A62 - 66
131(chain A and (resid 51 through 61 or (resid 62...A50 - 88
141(chain A and (resid 51 through 61 or (resid 62...A50 - 88
151(chain A and (resid 51 through 61 or (resid 62...A50 - 88
161(chain A and (resid 51 through 61 or (resid 62...A50 - 88
171(chain A and (resid 51 through 61 or (resid 62...A73
181(chain A and (resid 51 through 61 or (resid 62...A50 - 88
191(chain A and (resid 51 through 61 or (resid 62...A50 - 88
1101(chain A and (resid 51 through 61 or (resid 62...A50 - 88
1111(chain A and (resid 51 through 61 or (resid 62...A50 - 88
211(chain C and (resid 51 through 65 or (resid 66...C51 - 65
221(chain C and (resid 51 through 65 or (resid 66...C66
231(chain C and (resid 51 through 65 or (resid 66...C50 - 87
241(chain C and (resid 51 through 65 or (resid 66...C50 - 87
251(chain C and (resid 51 through 65 or (resid 66...C50 - 87
261(chain C and (resid 51 through 65 or (resid 66...C50 - 87
311(chain E and (resid 51 through 61 or (resid 62...E51 - 61
321(chain E and (resid 51 through 61 or (resid 62...E62 - 66
331(chain E and (resid 51 through 61 or (resid 62...E51 - 89
341(chain E and (resid 51 through 61 or (resid 62...E51 - 89
351(chain E and (resid 51 through 61 or (resid 62...E51 - 89
361(chain E and (resid 51 through 61 or (resid 62...E51 - 89
411(chain G and (resid 51 through 61 or (resid 62...G51 - 61
421(chain G and (resid 51 through 61 or (resid 62...G62 - 66
431(chain G and (resid 51 through 61 or (resid 62...G50 - 88
441(chain G and (resid 51 through 61 or (resid 62...G50 - 88
451(chain G and (resid 51 through 61 or (resid 62...G50 - 88
461(chain G and (resid 51 through 61 or (resid 62...G50 - 88
112(chain B and (resid 18 through 29 or (resid 30...B18 - 29
122(chain B and (resid 18 through 29 or (resid 30...B30
132(chain B and (resid 18 through 29 or (resid 30...B17 - 169
142(chain B and (resid 18 through 29 or (resid 30...B17 - 169
152(chain B and (resid 18 through 29 or (resid 30...B17 - 169
162(chain B and (resid 18 through 29 or (resid 30...B17 - 169
212(chain D and (resid 18 through 30 or resid 34...D18 - 30
222(chain D and (resid 18 through 30 or resid 34...D34 - 53
232(chain D and (resid 18 through 30 or resid 34...D54
242(chain D and (resid 18 through 30 or resid 34...D18 - 169
252(chain D and (resid 18 through 30 or resid 34...D0
262(chain D and (resid 18 through 30 or resid 34...D64 - 65
272(chain D and (resid 18 through 30 or resid 34...D18 - 169
282(chain D and (resid 18 through 30 or resid 34...D18 - 169
292(chain D and (resid 18 through 30 or resid 34...D18 - 169
2102(chain D and (resid 18 through 30 or resid 34...D18 - 169
312(chain F and (resid 18 through 60 or (resid 64...F18 - 60
322(chain F and (resid 18 through 60 or (resid 64...F64 - 65
332(chain F and (resid 18 through 60 or (resid 64...F14 - 171
342(chain F and (resid 18 through 60 or (resid 64...F14 - 171
352(chain F and (resid 18 through 60 or (resid 64...F14 - 171
362(chain F and (resid 18 through 60 or (resid 64...F14 - 171
412(chain H and (resid 18 through 30 or resid 34...H18 - 30
422(chain H and (resid 18 through 30 or resid 34...H34 - 53
432(chain H and (resid 18 through 30 or resid 34...H54
442(chain H and (resid 18 through 30 or resid 34...H18 - 170
452(chain H and (resid 18 through 30 or resid 34...H18 - 170
462(chain H and (resid 18 through 30 or resid 34...H18 - 170
472(chain H and (resid 18 through 30 or resid 34...H18 - 170

NCSアンサンブル:
ID
1
2

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要素

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タンパク質・ペプチド , 4種, 5分子 AGCEI

#1: タンパク質・ペプチド Core protein / Envelope protein E / Flavivirin protease NS2B regulatory subunit / Flavivirin protease NS3 ...Envelope protein E / Flavivirin protease NS2B regulatory subunit / Flavivirin protease NS3 catalytic subunit / Genome polyprotein / Matrix protein / Non-structural protein 1 / Non-structural protein 2A / Non-structural protein 2B / Non-structural protein 3 / Non-structural protein 4A / Non-structural protein 4B / Peptide 2k / Peptide pr / Protein prM / RNA-directed RNA polymerase NS5 / Serine protease NS3 / Serine protease subunit NS2B / Small envelope protein M


分子量: 4347.659 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) Zika virus (ジカ熱ウイルス) / 遺伝子: GP1, A2G93_72127gpGP1 / 発現宿主: Escherichia coli (大腸菌)
参照: UniProt: A0A2R4LVW1, flavivirin, nucleoside-triphosphate phosphatase, RNA helicase
#3: タンパク質・ペプチド Genome polyprotein


分子量: 4218.545 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Zika virus (ジカ熱ウイルス) / 発現宿主: Escherichia coli (大腸菌)
参照: UniProt: Q32ZE1, flavivirin, nucleoside-triphosphate phosphatase, RNA helicase, mRNA (guanine-N7)-methyltransferase, methyltransferase cap1, RNA-directed RNA polymerase
#5: タンパク質・ペプチド Serine protease subunit NS2B / Flavivirin protease NS2B regulatory subunit / Non-structural protein 2B


分子量: 4361.686 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Zika virus (ジカ熱ウイルス) / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: Q32ZE1
#8: タンパク質・ペプチド 3-PYRIDIN-4-YL-2,4-DIHYDRO-INDENO[1,2-.C.]PYRAZOLE


分子量: 809.959 Da / 分子数: 1 / 由来タイプ: 合成 / 由来: (合成) synthetic construct (人工物)

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タンパク質 , 4種, 4分子 BDFH

#2: タンパク質 Core protein / Envelope protein E / Flavivirin protease NS2B regulatory subunit / Flavivirin protease NS3 ...Envelope protein E / Flavivirin protease NS2B regulatory subunit / Flavivirin protease NS3 catalytic subunit / Genome polyprotein / Matrix protein / Non-structural protein 1 / Non-structural protein 2A / Non-structural protein 2B / Non-structural protein 3 / Non-structural protein 4A / Non-structural protein 4B / Peptide 2k / Peptide pr / Protein prM / RNA-directed RNA polymerase NS5 / Serine protease NS3 / Serine protease subunit NS2B / Small envelope protein M


分子量: 16342.598 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Zika virus (ジカ熱ウイルス) / 遺伝子: GP1, A2G93_63394gpGP1 / 発現宿主: Escherichia coli (大腸菌)
参照: UniProt: A0A142IX72, flavivirin, nucleoside-triphosphate phosphatase, RNA helicase
#4: タンパク質 Core protein / Envelope protein E / Flavivirin protease NS2B regulatory subunit / Flavivirin protease NS3 ...Envelope protein E / Flavivirin protease NS2B regulatory subunit / Flavivirin protease NS3 catalytic subunit / Genome polyprotein / Matrix protein / Non-structural protein 1 / Non-structural protein 2A / Non-structural protein 2B / Non-structural protein 3 / Non-structural protein 4A / Non-structural protein 4B / Peptide 2k / Peptide pr / Protein prM / RNA-directed RNA polymerase NS5 / Serine protease NS3 / Serine protease subunit NS2B / Small envelope protein M


分子量: 16213.484 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Zika virus (ジカ熱ウイルス) / 遺伝子: GP1, A2G93_63394gpGP1 / 発現宿主: Escherichia coli (大腸菌)
参照: UniProt: A0A142IX72, flavivirin, nucleoside-triphosphate phosphatase, RNA helicase
#6: タンパク質 Core protein / Envelope protein E / Flavivirin protease NS2B regulatory subunit / Flavivirin protease NS3 ...Envelope protein E / Flavivirin protease NS2B regulatory subunit / Flavivirin protease NS3 catalytic subunit / Genome polyprotein / Matrix protein / Non-structural protein 1 / Non-structural protein 2A / Non-structural protein 2B / Non-structural protein 3 / Non-structural protein 4A / Non-structural protein 4B / Peptide 2k / Peptide pr / Protein prM / RNA-directed RNA polymerase NS5 / Serine protease NS3 / Serine protease subunit NS2B / Small envelope protein M


分子量: 16944.318 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Zika virus (ジカ熱ウイルス) / 遺伝子: GP1, A2G93_63394gpGP1 / 発現宿主: Escherichia coli (大腸菌)
参照: UniProt: A0A142IX72, flavivirin, nucleoside-triphosphate phosphatase, RNA helicase
#7: タンパク質 Genome polyprotein / NS3 Protease


分子量: 16370.678 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Zika virus (ジカ熱ウイルス) / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: H8XX12

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非ポリマー , 1種, 371分子

#9: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 371 / 由来タイプ: 天然 / 式: H2O

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詳細

研究の焦点であるリガンドがあるかY

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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: 2.26 Å3/Da / 溶媒含有率: 45.55 %
結晶化温度: 291.15 K / 手法: 蒸気拡散法, ハンギングドロップ法
詳細: 0.2M Ammonium Sulfate, 0.1M Sodium Acetate Trihydrate pH 4.6, 30% Peg 2000

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データ収集

回折平均測定温度: 100 K / Serial crystal experiment: N
放射光源由来: シンクロトロン / サイト: Australian Synchrotron / ビームライン: MX2 / 波長: 0.95373 Å
検出器タイプ: ADSC QUANTUM 315r / 検出器: CCD / 日付: 2020年3月11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: 0.95373 Å / 相対比: 1
Reflection twinOperator: k,h,-l / Fraction: 0.15
反射解像度: 1.904→45.63 Å / Num. obs: 60261 / % possible obs: 99.39 % / 冗長度: 13.2 % / CC1/2: 0.997 / Rmerge(I) obs: 0.1312 / Rpim(I) all: 0.03716 / Rrim(I) all: 0.1365 / Net I/σ(I): 12.2
反射 シェル解像度: 1.904→1.972 Å / 冗長度: 12.7 % / Rmerge(I) obs: 0.8121 / Num. unique obs: 5640 / CC1/2: 0.925 / Rpim(I) all: 0.2344 / Rrim(I) all: 0.8459 / % possible all: 94.08

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解析

ソフトウェア
名称バージョン分類
PHENIX1.16_3549精密化
Aimlessデータスケーリング
PDB_EXTRACT3.27データ抽出
iMOSFLM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: 5GPI

5gpi


解像度: 1.904→45.63 Å / 交差検証法: THROUGHOUT / 立体化学のターゲット値: TWIN_LSQ_F
Rfactor反射数%反射
Rfree0.2286 2981 4.97 %
Rwork0.2092 57210 -
obs-60243 99.4 %
溶媒の処理溶媒モデル: FLAT BULK SOLVENT MODEL
原子変位パラメータBiso max: 145.19 Å2 / Biso mean: 45.9095 Å2 / Biso min: 23.6 Å2
精密化ステップサイクル: final / 解像度: 1.904→45.63 Å
タンパク質核酸リガンド溶媒全体
原子数5501 0 104 371 5976
Biso mean--73.4 50.76 -
残基数----765
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-ID数Refine-IDRmsタイプ
11A436X-RAY DIFFRACTION3.48TORSIONAL
12C436X-RAY DIFFRACTION3.48TORSIONAL
13E436X-RAY DIFFRACTION3.48TORSIONAL
14G436X-RAY DIFFRACTION3.48TORSIONAL
21B1720X-RAY DIFFRACTION3.48TORSIONAL
22D1720X-RAY DIFFRACTION3.48TORSIONAL
23F1720X-RAY DIFFRACTION3.48TORSIONAL
24H1720X-RAY DIFFRACTION3.48TORSIONAL
LS精密化 シェル解像度: 1.904→1.972 Å / Rfactor Rfree error: 0 /
Rfactor反射数
Rfree0.275 281
Rwork0.2947 5630
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)
15.33740.96372.74063.0533-1.10522.30530.0897-0.76831.0930.8508-0.08550.9012-0.6763-0.3187-0.08830.58330.08780.14340.6624-0.04730.3915-8.9807-0.538240.233
23.7946-2.14351.59637.6238-2.17790.92370.14890.3016-0.09960.8049-0.4879-0.6483-1.1144-0.21780.23370.73220.026-0.0630.51520.03170.29711.7774-5.277150.4588
33.6973-0.41364.7570.0983-0.36716.57040.0546-1.33490.09221.7733-0.37720.3565-0.13150.36820.14691.3447-0.0182-0.02890.73910.04660.21151.4756-18.134459.323
46.0150.58951.41958.8221-0.89880.45570.19740.1550.18920.7228-0.01520.6331-0.12281.0276-0.29191.0056-0.0817-0.00850.73050.13290.3013-4.6179-33.63950.0877
53.3549-1.05291.83141.6975-1.70822.7236-0.22940.0424-0.3494-0.71670.2193-0.00880.47690.05060.05960.646-0.15990.05860.7348-0.02440.229-9.8242-30.357935.3695
65.5518-0.3859-0.81311.57-1.04733.0567-0.25180.16250.67230.10730.26370.1479-0.6161-0.1985-0.10960.55760.04750.01470.5499-0.06590.2253-6.6541-4.410643.4568
73.54020.3518-0.75141.86070.0872.9665-0.27490.0105-0.1382-0.11680.180.1283-0.2931-0.18710.13480.5304-0.02430.03540.5252-0.03130.1237-2.6572-10.77736.9924
81.9714-1.92580.79056.5808-0.16563.8495-0.09520.15190.0917-0.56110.27940.4977-0.841-0.2364-0.23520.54590.00440.01270.620.06630.2817-3.0755-5.226732.3258
92.8312.3718-0.7286.87081.49552.7543-0.0881-0.5368-0.1624-0.4656-0.0691-0.5108-0.0188-0.26540.09190.47770.01530.00730.51010.02770.1454-3.2628-15.783933.0385
101.4940.31270.63511.855-1.29523.24630.2002-0.2789-0.19830.6485-0.1363-0.3897-0.35040.5457-0.13140.5499-0.0278-0.04730.6108-0.00070.23266.635-19.522342.9962
110.68931.1998-0.26962.5260.24611.29510.0593-0.2353-0.06971.0951-0.11850.27950.3518-0.0357-0.04470.6643-0.07890.01130.58880.03670.2172-4.7422-20.722849.3484
129.34542.76524.60826.8980.75142.83920.5275-0.5809-0.63750.87720.3807-0.95970.89980.1638-0.79760.7080.0842-0.09650.6088-0.0620.31745.8049-17.017649.4497
131.3165-0.00040.56761.69160.74981.00950.1311-0.15640.2410.1035-0.07930.30380.5208-0.42490.02370.6755-0.00680.0330.66430.05260.1511-6.411-23.611144.5574
144.7986-1.2037-1.00058.52862.08579.07731.315-0.31580.53870.9119-0.4274-1.1377-2.10471.7723-0.21440.8999-0.42970.08820.9360.05210.4483-21.6570.488267.9924
150.15380.480.01382.122-0.92031.58280.13060.8453-0.0939-0.8921-0.3022-0.37380.10150.34970.09660.62550.08540.00160.9918-0.10850.3141-29.2433-17.38652.9269
162.341-1.8516-1.28013.4144-0.07771.3199-0.06740.2288-0.25050.12650.15440.05570.29260.1041-0.13520.58440.1799-0.07080.9354-0.07820.2745-20.9285-28.670372.5636
173.99171.87132.42191.67941.64766.3914-0.5846-0.21260.2614-0.23560.11740.204-0.7599-0.04830.20550.6097-0.01720.01970.63610.13520.1833-27.4291-2.632963.3992
182.0023-1.8366-0.86212.781-0.57693.8823-0.6894-0.63760.80590.2510.3549-0.9212-0.20290.8160.41040.62460.0997-0.05980.88030.0662-0.0537-21.0658-4.667565.4663
193.2554-0.7251-1.10583.15760.65883.6124-0.44580.15720.00470.07060.2395-0.2241-0.55670.870.1840.4312-0.03190.01920.57110.00330.1517-28.484-9.696970.8864
201.8321-0.1719-0.93064.74840.84680.8721-0.221-0.02010.453-0.12180.4143-0.7654-0.59920.2892-0.24630.5786-0.1122-0.0270.7089-0.02040.1914-28.4748-4.248175.5968
211.9554-1.85360.81066.3052-1.20892.845-0.09860.0561-0.0906-0.15170.40710.16280.19560.4221-0.41750.46170.02750.02490.5445-0.00390.1545-28.1355-14.716874.8488
221.7561-0.16360.4966.17594.22324.9039-0.13150.3509-0.20330.13710.02920.1490.2528-0.1786-0.00770.4618-0.01430.00410.6128-0.02870.1878-37.4005-18.3164.6663
231.21540.4908-0.47412.91240.76750.5466-0.12590.2822-0.0163-0.64530.1896-0.1953-0.08690.116-0.06230.55670.10440.0590.7565-0.03910.2346-26.3259-18.846156.4561
242.03390.07790.21792.4123-0.74781.75380.23030.336-0.4533-0.1788-0.1562-0.07680.13760.676-0.01140.56750.04760.02320.7724-0.070.1836-25.9751-20.976362.2831
255.78162.3233-0.71158.89093.27188.81680.32480.51280.6372-0.28440.48240.6661-0.5479-1.4217-0.37280.3445-0.04490.01640.85570.23140.4123-15.1058-9.35310.9148
265.8241-1.70724.14165.24790.72274.09920.31960.4165-0.0945-1.63930.0558-0.06880.2110.2097-0.22930.4001-0.0519-0.02310.55660.09210.2165-8.4859-18.68982.0703
274.95033.597-2.35873.0428-1.4071.5889-0.59320.99890.727-1.59850.38870.3535-0.0119-0.1123-0.00890.57320.0134-0.02750.77080.04560.33513.9246-15.3502-5.6298
285.3391-1.8502-0.918.61153.99828.26150.22530.116-0.06990.2194-0.2984-1.241-0.43180.20420.16860.4325-0.02950.03390.610.17820.42618.0673-8.3016.2523
292.7871-1.9563-0.3671.61210.32020.06890.3198-0.80310.11270.6545-0.224-0.0286-0.27820.40620.12620.7286-0.2175-0.03120.61430.01640.221510.915-4.876220.9767
303.1427-1.3826-0.50049.59462.89259.22650.0557-0.19140.7998-0.20160.7061-1.299-0.23611.2679-0.72010.5388-0.11620.05830.5701-0.07250.425418.4245-1.751314.0336
310.92582.0774-0.59339.6378-1.17920.38330.02440.59930.127-0.0199-0.02231.03640.04960.03810.10040.4040.0436-0.02180.61620.06050.3017-14.4653-19.2089.9103
322.54160.09312.06898.9896-1.81142.06610.0747-0.01390.58670.4551-0.65150.4931-0.0992-0.49460.48660.44340.0030.07930.704-0.02820.1113-10.1815-7.572911.7064
332.16160.4737-1.59051.8193-0.23112.22360.1613-0.01470.05560.2958-0.12130.1495-0.0466-0.1871-0.04230.4159-0.0173-0.00660.43470.0220.1343-2.9088-15.352617.2889
342.83511.776-0.77542.6155-0.7160.2997-0.07340.039-0.043-0.04750.0535-0.0548-0.00480.06090.03130.3422-0.00350.00440.44340.0420.14734.8536-11.4416.2804
354.103-0.47930.13892.15261.84682.7070.14090.07430.0216-0.2815-0.05110.4847-0.0166-0.5983-0.04020.3743-0.036-0.01990.45370.09080.2285-38.1364-40.21987.7478
363.1521.78250.10534.38971.790.8676-0.73311.91210.1342-1.9580.41550.44260.0725-0.35280.34220.78290.07360.0290.77920.00560.1951-21.8131-46.4875-4.9393
372.00160.73289.63425.61683.16842.0009-0.6827-0.22190.6665-0.2101-0.5789-0.1096-0.1988-0.17130.40170.4233-0.10420.07330.6111-0.04610.1829-7.4858-38.88785.1926
380.1213-0.43170.62763.3279-1.86083.31130.3921-0.80360.01570.361-0.4047-0.1953-0.14780.9015-0.00040.5779-0.1543-0.01210.57560.00840.1973-10.6369-34.703819.551
393.38432.522-0.36356.52263.47193.69580.0665-0.08810.37110.6362-0.18750.98860.5308-0.39060.07660.3678-0.0121-0.02790.52660.05540.21-37.4168-40.74888.4523
403.93282.11592.14581.6702-0.02633.8062-0.19650.42050.9796-0.2308-0.04380.7043-0.3276-0.64910.27460.3990.00150.02070.55460.04220.2927-35.6227-34.9399.8334
413.00391.9077-0.50922.7497-0.06473.2744-0.0714-0.06230.41440.43110.1560.35570.0312-0.3469-0.0590.39560.02160.03140.49240.03550.1678-34.5936-41.259818.6748
424.09390.1447-2.20560.76180.12681.8508-0.03580.0634-0.3543-0.0274-0.1288-0.03960.2882-0.11540.11380.4001-0.0041-0.01740.38390.0390.1474-23.0642-47.525514.6457
432.95390.9783-1.05342.658-0.08030.3816-0.04720.1792-0.0403-0.08930.0742-0.01440.1014-0.0106-0.01730.36530.0046-0.00030.40130.02030.1132-19.9532-41.51696.0436
442.4499-0.46561.32912.46041.86112.56390.0244-0.3090.1761-0.42880.0454-0.3269-0.01440.2209-0.00730.36850.13170.06930.54190.02190.2183-16.7266-38.896910.6895
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 50 through 54 )A50 - 54
2X-RAY DIFFRACTION2chain 'A' and (resid 55 through 59 )A55 - 59
3X-RAY DIFFRACTION3chain 'A' and (resid 60 through 69 )A60 - 69
4X-RAY DIFFRACTION4chain 'A' and (resid 70 through 74 )A70 - 74
5X-RAY DIFFRACTION5chain 'A' and (resid 75 through 88 )A75 - 88
6X-RAY DIFFRACTION6chain 'B' and (resid 17 through 42 )B17 - 42
7X-RAY DIFFRACTION7chain 'B' and (resid 43 through 53 )B43 - 53
8X-RAY DIFFRACTION8chain 'B' and (resid 54 through 71 )B54 - 71
9X-RAY DIFFRACTION9chain 'B' and (resid 72 through 79 )B72 - 79
10X-RAY DIFFRACTION10chain 'B' and (resid 80 through 94 )B80 - 94
11X-RAY DIFFRACTION11chain 'B' and (resid 95 through 136 )B95 - 136
12X-RAY DIFFRACTION12chain 'B' and (resid 137 through 145 )B137 - 145
13X-RAY DIFFRACTION13chain 'B' and (resid 146 through 169 )B146 - 169
14X-RAY DIFFRACTION14chain 'C' and (resid 50 through 54 )C50 - 54
15X-RAY DIFFRACTION15chain 'C' and (resid 55 through 74 )C55 - 74
16X-RAY DIFFRACTION16chain 'C' and (resid 75 through 87 )C75 - 87
17X-RAY DIFFRACTION17chain 'D' and (resid 18 through 27 )D18 - 27
18X-RAY DIFFRACTION18chain 'D' and (resid 28 through 42 )D28 - 42
19X-RAY DIFFRACTION19chain 'D' and (resid 43 through 53 )D43 - 53
20X-RAY DIFFRACTION20chain 'D' and (resid 54 through 71 )D54 - 71
21X-RAY DIFFRACTION21chain 'D' and (resid 72 through 79 )D72 - 79
22X-RAY DIFFRACTION22chain 'D' and (resid 80 through 94 )D80 - 94
23X-RAY DIFFRACTION23chain 'D' and (resid 95 through 118 )D95 - 118
24X-RAY DIFFRACTION24chain 'D' and (resid 119 through 169 )D119 - 169
25X-RAY DIFFRACTION25chain 'E' and (resid 51 through 55 )E51 - 55
26X-RAY DIFFRACTION26chain 'E' and (resid 56 through 60 )E56 - 60
27X-RAY DIFFRACTION27chain 'E' and (resid 61 through 70 )E61 - 70
28X-RAY DIFFRACTION28chain 'E' and (resid 71 through 75 )E71 - 75
29X-RAY DIFFRACTION29chain 'E' and (resid 76 through 83 )E76 - 83
30X-RAY DIFFRACTION30chain 'E' and (resid 84 through 89 )E84 - 89
31X-RAY DIFFRACTION31chain 'F' and (resid 14 through 26 )F14 - 26
32X-RAY DIFFRACTION32chain 'F' and (resid 27 through 42 )F27 - 42
33X-RAY DIFFRACTION33chain 'F' and (resid 43 through 94 )F43 - 94
34X-RAY DIFFRACTION34chain 'F' and (resid 95 through 171 )F95 - 171
35X-RAY DIFFRACTION35chain 'G' and (resid 50 through 59 )G50 - 59
36X-RAY DIFFRACTION36chain 'G' and (resid 60 through 69 )G60 - 69
37X-RAY DIFFRACTION37chain 'G' and (resid 70 through 74 )G70 - 74
38X-RAY DIFFRACTION38chain 'G' and (resid 75 through 88 )G75 - 88
39X-RAY DIFFRACTION39chain 'H' and (resid 18 through 28 )H18 - 28
40X-RAY DIFFRACTION40chain 'H' and (resid 29 through 42 )H29 - 42
41X-RAY DIFFRACTION41chain 'H' and (resid 43 through 71 )H43 - 71
42X-RAY DIFFRACTION42chain 'H' and (resid 72 through 94 )H72 - 94
43X-RAY DIFFRACTION43chain 'H' and (resid 95 through 155 )H95 - 155
44X-RAY DIFFRACTION44chain 'H' and (resid 156 through 170 )H156 - 170

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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