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- PDB-6l4z: Crystal structure of Zika NS2B-NS3 protease with compound 6 -

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基本情報

登録情報
データベース: PDB / ID: 6l4z
タイトルCrystal structure of Zika NS2B-NS3 protease with compound 6
要素(Genome polyprotein) x 7
キーワードVIRAL PROTEIN / Viral protease / Protease inhibitor complex
機能・相同性
機能・相同性情報


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 ...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 / mRNA (guanine-N7)-methyltransferase / methyltransferase cap1 / clathrin-dependent endocytosis of virus by host cell / mRNA (nucleoside-2'-O-)-methyltransferase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / RNA helicase activity / host cell perinuclear region of cytoplasm / protein dimerization activity / 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 / induction by virus of host autophagy / symbiont entry into host cell / RNA-directed RNA polymerase / viral RNA genome replication / serine-type endopeptidase activity / RNA-dependent RNA polymerase activity / virus-mediated perturbation of host defense response / fusion of virus membrane with host endosome membrane / lipid binding / viral envelope / host cell nucleus / virion attachment to host cell / GTP binding / structural molecule activity / virion membrane / ATP hydrolysis activity / proteolysis / extracellular region / ATP binding / membrane / metal ion binding
類似検索 - 分子機能
Thrombin, subunit H - #120 / Flavivirus capsid protein C superfamily / Flavivirus non-structural protein NS2B / Genome polyprotein, Flavivirus / : / Flavivirus non-structural protein NS4A / Flavivirus non-structural protein NS2B / Flavivirus capsid protein C / Flavivirus non-structural protein NS4B / mRNA cap 0/1 methyltransferase ...Thrombin, subunit H - #120 / Flavivirus capsid protein C superfamily / Flavivirus non-structural protein NS2B / Genome polyprotein, Flavivirus / : / Flavivirus non-structural protein NS4A / Flavivirus non-structural protein NS2B / Flavivirus capsid protein C / Flavivirus non-structural protein NS4B / mRNA cap 0/1 methyltransferase / Flavivirus capsid protein C / 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 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 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 / : / Flavivirus NS3 helicase, C-terminal helical domain / 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 / Trypsin-like serine proteases / 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 / Thrombin, subunit H / 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 / Beta Barrel / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
類似検索 - ドメイン・相同性
4-(hydroxymethyl)benzoic acid / Genome polyprotein / Genome polyprotein
類似検索 - 構成要素
生物種Zika virus (ジカ熱ウイルス)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 1.9 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: Antiviral Res. / 年: 2020
タイトル: Identification and structural characterization of small molecule fragments targeting Zika virus NS2B-NS3 protease.
著者: Quek, J.P. / Liu, S. / Zhang, Z. / Li, Y. / Ng, E.Y. / Loh, Y.R. / Hung, A.W. / Luo, D. / Kang, C.
履歴
登録2019年10月21日登録サイト: PDBJ / 処理サイト: PDBJ
改定 1.02020年7月15日Provider: repository / タイプ: Initial release
改定 1.12023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

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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: Genome polyprotein
B: Genome polyprotein
C: Genome polyprotein
D: Genome polyprotein
E: Genome polyprotein
F: Genome polyprotein
G: Genome polyprotein
H: Genome polyprotein
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)83,4109
ポリマ－83,2588
非ポリマー1521
水3,135174
1
A: Genome polyprotein
B: Genome polyprotein


分子量 (理論値)分子数
合計 (水以外)20,7752
ポリマ－20,7752
非ポリマー00
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area3760 Å2
ΔGint-27 kcal/mol
Surface area9130 Å2
手法PISA
2
C: Genome polyprotein
D: Genome polyprotein


分子量 (理論値)分子数
合計 (水以外)20,4742
ポリマ－20,4742
非ポリマー00
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area3820 Å2
ΔGint-28 kcal/mol
Surface area8580 Å2
手法PISA
3
E: Genome polyprotein
F: Genome polyprotein


分子量 (理論値)分子数
合計 (水以外)20,4882
ポリマ－20,4882
非ポリマー00
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area3750 Å2
ΔGint-28 kcal/mol
Surface area9140 Å2
手法PISA
4
G: Genome polyprotein
H: Genome polyprotein
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)21,6723
ポリマ－21,5202
非ポリマー1521
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area3810 Å2
ΔGint-23 kcal/mol
Surface area9650 Å2
手法PISA
単位格子
Length a, b, c (Å)59.549, 59.525, 214.556
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 74 or (resid 75...
21(chain C and (resid 51 through 61 or (resid 62...
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 19 through 27 or resid 34...
22(chain D and (resid 19 through 27 or resid 34...
32(chain F and (resid 19 through 27 or resid 34...
42(chain H and (resid 19 through 58 or (resid 59...

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
111METMETLEULEU(chain A and (resid 51 through 74 or (resid 75...AA51 - 742 - 25
121ASPASPASPASP(chain A and (resid 51 through 74 or (resid 75...AA7526
131ASPASPVALVAL(chain A and (resid 51 through 74 or (resid 75...AA50 - 871 - 38
141ASPASPVALVAL(chain A and (resid 51 through 74 or (resid 75...AA50 - 871 - 38
151ASPASPVALVAL(chain A and (resid 51 through 74 or (resid 75...AA50 - 871 - 38
161ASPASPVALVAL(chain A and (resid 51 through 74 or (resid 75...AA50 - 871 - 38
211METMETTRPTRP(chain C and (resid 51 through 61 or (resid 62...CC51 - 611 - 11
221GLUGLUGLUGLU(chain C and (resid 51 through 61 or (resid 62...CC62 - 6612 - 16
231METMETVALVAL(chain C and (resid 51 through 61 or (resid 62...CC51 - 871 - 37
241METMETVALVAL(chain C and (resid 51 through 61 or (resid 62...CC51 - 871 - 37
251METMETVALVAL(chain C and (resid 51 through 61 or (resid 62...CC51 - 871 - 37
261METMETVALVAL(chain C and (resid 51 through 61 or (resid 62...CC51 - 871 - 37
311METMETTRPTRP(chain E and (resid 51 through 61 or (resid 62...EE51 - 612 - 12
321GLUGLUGLUGLU(chain E and (resid 51 through 61 or (resid 62...EE62 - 6613 - 17
331ASPASPVALVAL(chain E and (resid 51 through 61 or (resid 62...EE50 - 871 - 38
341ASPASPVALVAL(chain E and (resid 51 through 61 or (resid 62...EE50 - 871 - 38
351ASPASPVALVAL(chain E and (resid 51 through 61 or (resid 62...EE50 - 871 - 38
361ASPASPVALVAL(chain E and (resid 51 through 61 or (resid 62...EE50 - 871 - 38
411METMETTRPTRP(chain G and (resid 51 through 61 or (resid 62...GG51 - 612 - 12
421GLUGLUGLUGLU(chain G and (resid 51 through 61 or (resid 62...GG62 - 6613 - 17
431ASPASPGLUGLU(chain G and (resid 51 through 61 or (resid 62...GG50 - 891 - 40
441ASPASPGLUGLU(chain G and (resid 51 through 61 or (resid 62...GG50 - 891 - 40
451ASPASPGLUGLU(chain G and (resid 51 through 61 or (resid 62...GG50 - 891 - 40
461ASPASPGLUGLU(chain G and (resid 51 through 61 or (resid 62...GG50 - 891 - 40
471ASPASPGLUGLU(chain G and (resid 51 through 61 or (resid 62...GG50 - 891 - 40
481ASPASPGLUGLU(chain G and (resid 51 through 61 or (resid 62...GG50 - 891 - 40
491ASPASPGLUGLU(chain G and (resid 51 through 61 or (resid 62...GG50 - 891 - 40
4101ASPASPGLUGLU(chain G and (resid 51 through 61 or (resid 62...GG50 - 891 - 40
4111ASPASPGLUGLU(chain G and (resid 51 through 61 or (resid 62...GG50 - 891 - 40
112THRTHRTHRTHR(chain B and (resid 19 through 27 or resid 34...BB19 - 274 - 12
122THRTHRLEULEU(chain B and (resid 19 through 27 or resid 34...BB34 - 5819 - 43
132ARGARGARGARG(chain B and (resid 19 through 27 or resid 34...BB5944
142GLYGLYARGARG(chain B and (resid 19 through 27 or resid 34...BB16 - 1701 - 155
152GLYGLYARGARG(chain B and (resid 19 through 27 or resid 34...BB16 - 1701 - 155
162GLYGLYARGARG(chain B and (resid 19 through 27 or resid 34...BB16 - 1701 - 155
172GLYGLYARGARG(chain B and (resid 19 through 27 or resid 34...BB16 - 1701 - 155
212THRTHRTHRTHR(chain D and (resid 19 through 27 or resid 34...DD19 - 272 - 10
222THRTHRGLYGLY(chain D and (resid 19 through 27 or resid 34...DD34 - 10317 - 86
232GLUGLUALAALA(chain D and (resid 19 through 27 or resid 34...DD104 - 10687 - 89
242THRTHRARGARG(chain D and (resid 19 through 27 or resid 34...DD18 - 1701 - 153
252THRTHRARGARG(chain D and (resid 19 through 27 or resid 34...DD18 - 1701 - 153
262THRTHRARGARG(chain D and (resid 19 through 27 or resid 34...DD18 - 1701 - 153
272THRTHRARGARG(chain D and (resid 19 through 27 or resid 34...DD18 - 1701 - 153
282THRTHRARGARG(chain D and (resid 19 through 27 or resid 34...DD18 - 1701 - 153
312THRTHRTHRTHR(chain F and (resid 19 through 27 or resid 34...FF19 - 271 - 9
322THRTHRGLUGLU(chain F and (resid 19 through 27 or resid 34...FF34 - 10416 - 86
332ARGARGALAALA(chain F and (resid 19 through 27 or resid 34...FF105 - 10687 - 88
342THRTHRARGARG(chain F and (resid 19 through 27 or resid 34...FF19 - 1701 - 152
352THRTHRARGARG(chain F and (resid 19 through 27 or resid 34...FF19 - 1701 - 152
362THRTHRARGARG(chain F and (resid 19 through 27 or resid 34...FF19 - 1701 - 152
372THRTHRARGARG(chain F and (resid 19 through 27 or resid 34...FF19 - 1701 - 152
382THRTHRARGARG(chain F and (resid 19 through 27 or resid 34...FF19 - 1701 - 152
412THRTHRLEULEU(chain H and (resid 19 through 58 or (resid 59...HH19 - 588 - 47
422ARGARGARGARG(chain H and (resid 19 through 58 or (resid 59...HH5948
432GLUGLUARGARG(chain H and (resid 19 through 58 or (resid 59...HH12 - 1701 - 159
442GLUGLUARGARG(chain H and (resid 19 through 58 or (resid 59...HH12 - 1701 - 159
452GLUGLUARGARG(chain H and (resid 19 through 58 or (resid 59...HH12 - 1701 - 159
462GLUGLUARGARG(chain H and (resid 19 through 58 or (resid 59...HH12 - 1701 - 159

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 , 3種, 4分子 AECG

#1: タンパク質・ペプチド Genome polyprotein


分子量: 4218.545 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) / 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
#3: タンパク質・ペプチド Genome polyprotein / NS2B Cofactor


分子量: 4103.458 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
#6: タンパク質・ペプチド Genome polyprotein / NS2B Cofactor


分子量: 4476.773 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

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タンパク質 , 4種, 4分子 BDFH

#2: タンパク質 Genome polyprotein / NS3 Protease


分子量: 16556.846 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, UniProt: Q32ZE1*PLUS
#4: 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, UniProt: Q32ZE1*PLUS
#5: タンパク質 Genome polyprotein


分子量: 16269.574 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, UniProt: Q32ZE1*PLUS
#7: タンパク質 Genome polyprotein / NS3 Protease


分子量: 17043.447 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, UniProt: Q32ZE1*PLUS

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非ポリマー , 2種, 175分子

#8: 化合物 ChemComp-E5X / 4-(hydroxymethyl)benzoic acid / 4-(ヒドロキシメチル)安息香酸


分子量: 152.147 Da / 分子数: 1 / 由来タイプ: 合成 / 式: C8H8O3 / タイプ: SUBJECT OF INVESTIGATION
#9: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 174 / 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: 2.29 Å3/Da / 溶媒含有率: 46.2 %
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: 0.2 M Ammonium sulfate, 0.1 M Sodium acetate trihydrate pH 4.6, 30% PEG2000

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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: MX1 / 波長: 0.9537 Å
検出器タイプ: ADSC QUANTUM 210r / 検出器: CCD / 日付: 2017年2月28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: 0.9537 Å / 相対比: 1
Reflection twinOperator: k,h,-l / Fraction: 0.44
反射解像度: 1.9→45.76 Å / Num. obs: 61183 / % possible obs: 99.35 % / 冗長度: 1.1 % / CC1/2: 0.812 / Net I/σ(I): 14.09
反射 シェル解像度: 1.9→1.968 Å / Mean I/σ(I) obs: 1.69 / Num. unique obs: 6015 / CC1/2: 0.27

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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_EXTRACT3.25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: 5gpi

5gpi


解像度: 1.9→45.76 Å / 交差検証法: NONE / σ(F): 16.74 / 位相誤差: 21.8
Rfactor反射数%反射
Rfree0.2261 3015 4.93 %
Rwork0.1798 --
obs0.1912 61146 99.94 %
溶媒の処理減衰半径: 0.9 Å / VDWプローブ半径: 1.11 Å
原子変位パラメータBiso max: 90.31 Å2 / Biso mean: 32.1917 Å2 / Biso min: 13.62 Å2
精密化ステップサイクル: final / 解像度: 1.9→45.76 Å
タンパク質核酸リガンド溶媒全体
原子数5611 0 11 174 5796
Biso mean--32.38 31.4 -
残基数----761
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-ID数Refine-IDRmsタイプ
11A440X-RAY DIFFRACTION6.603TORSIONAL
12C440X-RAY DIFFRACTION6.603TORSIONAL
13E440X-RAY DIFFRACTION6.603TORSIONAL
14G440X-RAY DIFFRACTION6.603TORSIONAL
21B1696X-RAY DIFFRACTION6.603TORSIONAL
22D1696X-RAY DIFFRACTION6.603TORSIONAL
23F1696X-RAY DIFFRACTION6.603TORSIONAL
24H1696X-RAY DIFFRACTION6.603TORSIONAL
LS精密化 シェル

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 20

解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9004-1.93320.31751560.28452882303895
1.9332-1.96830.29281370.26452843298095
1.9683-2.00610.251530.25812886303995
2.0061-2.0470.27431550.26022827298295
2.047-2.09150.27271430.26072821296495
2.0915-2.14010.28981570.2452908306595
2.1401-2.19350.28931730.23582848302194
2.1935-2.25280.26961400.23142867300795
2.2528-2.3190.24871480.2222873302195
2.319-2.39370.25461370.22162898303595
2.3937-2.47910.23481540.2272942309695
2.4791-2.57820.22871640.21052809297394
2.5782-2.69520.2621320.20982946307896
2.6952-2.8370.25931490.19522903305295
2.837-3.01420.22151450.18962868301395
3.0142-3.2460.19941420.18562948309095
3.246-3.5710.23551560.17782909306595
3.571-4.0840.23221700.16432944311495
4.084-5.13120.19641520.13182982313495
5.1312-20.10330.21441490.14793136328595
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)
15.909-1.5878-0.877.22371.64494.9890.05950.6141-0.53070.007-0.0207-0.93930.28810.5726-0.31230.4660.0743-0.10480.0003-0.06360.388939.204263.310842.0349
21.97631.4599-0.66712.281-1.51821.07370.3082-0.53660.08140.576-0.28990.52240.0718-0.23-0.18330.20780.0058-0.01520.2167-0.01230.234928.043377.690955.9137
34.77340.9798-1.71835.4713-1.4572.2984-0.44160.11840.5091-0.06740.1137-0.0791-0.27480.2070.18880.32120.0185-0.03020.1574-0.01250.234935.296797.380748.5026
43.72440.53430.78750.9468-1.05945.7857-0.45520.33860.3295-0.33150.24090.2694-0.02460.70010.12330.26-0.09-0.01620.25360.06510.177339.829692.224233.9048
57.6008-1.585-1.19872.6751-0.8244.2332-0.05010.4034-0.69040.0385-0.0198-0.26740.4483-0.15210.0690.38040.0117-0.02660.1455-0.02920.24736.587864.872444.3491
63.24330.9284-0.3851.9850.22640.79570.06090.0862-0.34020.08240.0168-0.20780.32910.0069-0.06460.25760.03-0.04010.143-0.02850.177734.845169.752439.2418
72.73444.3597-0.48952.0233-2.32733.2947-0.0280.1877-0.1521-0.11170.1315-0.50970.1544-0.1739-0.09370.32410.0323-0.01660.2149-0.03860.114832.34772.985731.9623
81.51390.6372-0.34442.57190.8014-0.01160.0067-0.08750.14170.0823-0.03880.2484-0.0058-0.07740.02180.22390.0128-0.02660.16880.00330.129929.541482.816247.9397
92.24830.91090.1722.24520.22970.63190.04430.02470.081-0.0241-0.0420.1773-0.1156-0.0083-0.03510.26350.0265-0.03190.1324-0.00030.09932.548884.542345.3323
109.60782.50044.99114.85252.76116.5510.18090.2034-0.1173-0.009-0.1267-0.06760.00460.11440.02930.21440.0567-0.0030.09620.04260.17435.353787.082642.628
115.95440.91560.42332.0942.80563.8333-0.65250.4276-0.56440.7540.2563-0.0409-0.02211.87180.25770.39490.11780.07220.606-0.03540.295742.010672.26927.5221
124.0026-0.87873.14468.22520.50642.6398-0.7711.96830.4897-0.8818-0.6838-0.0530.4275-0.10661.17210.5372-0.14770.04770.6591-0.00660.255930.37478.2497-6.4477
131.17580.39310.38574.2999-1.27840.77530.13230.3681-0.17040.31790.06760.59780.30210.1608-0.2390.429-0.0265-0.06960.3555-0.02760.342716.24967.344511.6853
142.5885-1.5801-1.10151.81432.07442.32420.07870.337-0.0098-0.3922-0.0073-0.2016-0.28210.1267-0.06070.46730.03840.04270.37290.00720.16838.282571.684712.8154
157.3841-0.15351.30483.67421.39650.87990.48140.5125-0.59710.0337-0.0877-0.32320.24520.3461-0.39140.45980.1143-0.01680.3453-0.0130.15540.844973.135521.9411
162.6660.95940.77460.64120.53970.82360.07820.52840.0103-0.5089-0.05640.2704-0.40720.19750.07470.68840.1197-0.04620.3255-0.02610.169227.603278.648714.1737
173.175-0.6399-0.23092.4017-0.4833-0.0197-0.00180.4564-0.2335-0.2443-0.06470.2355-0.1526-0.00450.06030.4387-0.0435-0.03260.3395-0.07190.208624.616570.04535.3791
184.0512-0.4157-0.47180.757-1.42083.4023-0.15910.475-0.3312-0.8253-0.19450.178-0.46260.24190.22040.67540.0558-0.10.3824-0.06970.12526.486575.44596.8992
192.0829-0.8605-0.8630.6134-0.2482.0023-0.35040.028-0.2165-0.9689-0.03920.4812-0.4245-0.26730.5240.28130.0471-0.08880.3509-0.04890.230721.522269.088810.1401
205.08790.6353-1.79133.3041-3.29393.623-0.2376-0.52550.1668-0.0114-0.2037-0.53940.43641.12570.31560.44450.0624-0.04290.4306-0.07650.126141.961348.737-8.6662
213.15773.8543-3.87286.8581-3.58868.95980.2268-2.2448-0.3808-0.1490.05360.09660.4731.06960.31320.33730.0142-0.06880.5037-0.0170.322329.814839.95825.5517
220.5473-0.20.85240.5528-0.70461.6152-0.2442-0.2149-0.05920.2404-0.19870.0736-0.61110.3254-0.16380.6320.13630.16920.83870.07070.115122.326248.1636.5096
233.21061.6028-2.98144.0531-2.64793.14150.38720.5260.2918-0.1860.090.8109-0.1546-0.2754-0.39630.31520.1280.0170.45350.0230.257313.851752.8939-14.2435
243.09830.65770.54570.9957-0.82895.14080.1671-0.06290.33-0.0817-0.12730.1716-0.87170.34130.0320.4656-0.0682-0.04060.30250.00470.189141.309154.901-10.0834
251.64380.21280.38643.1107-1.1293.39670.1519-0.32050.11270.4494-0.0928-0.09120.0581-0.0584-0.0330.2356-0.0153-0.02360.2751-0.0430.130834.790247.5648-14.4082
266.2481-0.03842.20575.03242.05483.45810.25760.68950.646-0.19730.1682-0.76420.10130.5272-0.41110.28730.00550.05070.1783-0.01870.266939.817547.7539-21.6651
273.1156-0.7004-1.18521.341-0.17970.57180.1014-0.082-0.343-0.0973-0.15570.1283-0.04190.09780.02540.2721-0.0322-0.0130.2415-0.00720.122326.530341.6161-14.3473
282.6370.8619-0.47542.5605-0.60230.10690.4149-0.83130.22150.5645-0.3091-0.01370.0312-0.1111-0.10140.3106-0.01190.01430.3377-0.04560.129425.788948.102-1.7588
291.07590.0574-0.00193.57971.08981.284-0.0482-0.2067-0.07370.36690.12220.0213-0.2282-0.0382-0.06430.32780.01270.00130.3369-0.010.134523.676847.22-7.7594
305.8749-2.7673-1.79156.41720.44122.2482-0.35390.09610.32920.50180.39120.02530.5025-0.30440.07340.2719-0.0356-0.00450.3946-0.00890.101820.16250.2397-10.1781
315.52791.11370.75870.9226-0.81671.47090.17740.487-0.98940.1013-0.0803-0.8990.79240.3445-0.29250.56060.1007-0.15130.2318-0.06510.2647.848629.025140.198
322.887-1.91090.83682.3068-0.66890.2621-0.0705-0.9606-0.2567-0.0340.1574-0.14170.4612-0.05810.08310.3844-0.1366-0.05390.16710.07910.1919-2.338533.648950.1777
332.98052.1351-1.27254.529-0.73143.05880.2365-0.32710.10481.0024-0.0639-0.0097-0.18670.002-0.22480.29590.1045-0.05730.19300.22980.960751.929156.2818
346.0875-0.435-0.68588.59140.98825.06430.03720.20860.49670.06520.2786-0.9274-0.43930.5416-0.10390.2505-0.0637-0.01550.22610.01310.22811.106159.298136.2466
352.10092.0290.9753.52972.05081.7388-0.140.34540.0751-0.07640.5221-0.0527-0.11740.82580.05260.2061-0.03350.07910.27020.01650.4066-12.342925.993342.6155
362.62930.75540.91561.80360.30161.25890.06070.003-0.3541-0.00310.069-0.27260.2542-0.0253-0.07410.2847-0.0009-0.00030.1134-0.03330.12723.561536.762640.7118
376.0563-0.25542.14830.11960.59725.46261.10870.205-0.87550.7119-0.0717-0.09721.93060.6306-0.41380.86260.1621-0.15130.4201-0.08260.27964.334529.428233.4244
381.33920.2910.52291.39991.08141.478-0.14360.25020.1345-0.06170.15770.08830.05560.05960.03070.2621-0.006-0.01340.16640.02350.1185-2.731745.996437.4258
394.6964-2.602-0.40123.89311.25940.5011-0.1985-0.2337-0.09010.47130.1893-0.27180.2476-0.0267-0.12620.3373-0.0189-0.03970.12020.02110.10755.146140.186453.3038
402.11970.61620.16421.88220.37132.3878-0.13290.02750.24460.35430.16260.0635-0.35530.04320.10520.19880.0076-0.03260.14510.00320.12972.212554.150550.4911
411.62250.73951.06541.2828-0.00681.6011-0.0304-0.00710.0922-0.1373-0.02440.0768-0.1756-0.01090.02660.27180.0106-0.01820.12530.00030.10962.659349.714946.0489
424.83061.94682.16321.53141.40361.71780.28450.14970.18930.1776-0.24190.08970.1999-0.05520.14620.24190.0105-0.03070.12570.02780.14285.672652.63143.9919
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 69 )A55 - 69
3X-RAY DIFFRACTION3chain 'A' and (resid 70 through 74 )A70 - 74
4X-RAY DIFFRACTION4chain 'A' and (resid 75 through 87 )A75 - 87
5X-RAY DIFFRACTION5chain 'B' and (resid 16 through 32 )B16 - 32
6X-RAY DIFFRACTION6chain 'B' and (resid 33 through 62 )B33 - 62
7X-RAY DIFFRACTION7chain 'B' and (resid 63 through 79 )B63 - 79
8X-RAY DIFFRACTION8chain 'B' and (resid 80 through 118 )B80 - 118
9X-RAY DIFFRACTION9chain 'B' and (resid 119 through 155 )B119 - 155
10X-RAY DIFFRACTION10chain 'B' and (resid 156 through 170 )B156 - 170
11X-RAY DIFFRACTION11chain 'C' and (resid 51 through 60 )C51 - 60
12X-RAY DIFFRACTION12chain 'C' and (resid 61 through 65 )C61 - 65
13X-RAY DIFFRACTION13chain 'C' and (resid 66 through 87 )C66 - 87
14X-RAY DIFFRACTION14chain 'D' and (resid 18 through 53 )D18 - 53
15X-RAY DIFFRACTION15chain 'D' and (resid 54 through 71 )D54 - 71
16X-RAY DIFFRACTION16chain 'D' and (resid 72 through 94 )D72 - 94
17X-RAY DIFFRACTION17chain 'D' and (resid 95 through 136 )D95 - 136
18X-RAY DIFFRACTION18chain 'D' and (resid 137 through 155 )D137 - 155
19X-RAY DIFFRACTION19chain 'D' and (resid 156 through 170 )D156 - 170
20X-RAY DIFFRACTION20chain 'E' and (resid 50 through 59 )E50 - 59
21X-RAY DIFFRACTION21chain 'E' and (resid 60 through 64 )E60 - 64
22X-RAY DIFFRACTION22chain 'E' and (resid 65 through 69 )E65 - 69
23X-RAY DIFFRACTION23chain 'E' and (resid 70 through 87 )E70 - 87
24X-RAY DIFFRACTION24chain 'F' and (resid 19 through 34 )F19 - 34
25X-RAY DIFFRACTION25chain 'F' and (resid 35 through 53 )F35 - 53
26X-RAY DIFFRACTION26chain 'F' and (resid 54 through 71 )F54 - 71
27X-RAY DIFFRACTION27chain 'F' and (resid 72 through 94 )F72 - 94
28X-RAY DIFFRACTION28chain 'F' and (resid 95 through 118 )F95 - 118
29X-RAY DIFFRACTION29chain 'F' and (resid 119 through 155 )F119 - 155
30X-RAY DIFFRACTION30chain 'F' and (resid 156 through 170 )F156 - 170
31X-RAY DIFFRACTION31chain 'G' and (resid 50 through 54 )G50 - 54
32X-RAY DIFFRACTION32chain 'G' and (resid 55 through 59 )G55 - 59
33X-RAY DIFFRACTION33chain 'G' and (resid 60 through 74 )G60 - 74
34X-RAY DIFFRACTION34chain 'G' and (resid 75 through 89 )G75 - 89
35X-RAY DIFFRACTION35chain 'H' and (resid 12 through 20 )H12 - 20
36X-RAY DIFFRACTION36chain 'H' and (resid 21 through 53 )H21 - 53
37X-RAY DIFFRACTION37chain 'H' and (resid 54 through 66 )H54 - 66
38X-RAY DIFFRACTION38chain 'H' and (resid 67 through 94 )H67 - 94
39X-RAY DIFFRACTION39chain 'H' and (resid 95 through 106 )H95 - 106
40X-RAY DIFFRACTION40chain 'H' and (resid 107 through 118 )H107 - 118
41X-RAY DIFFRACTION41chain 'H' and (resid 119 through 155 )H119 - 155
42X-RAY DIFFRACTION42chain '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