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- PDB-5zmq: Crystal structure of Zika NS3 protease with phenylacetyl-Lys-Lys-... -

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基本情報

登録情報
データベース: PDB / ID: 5zmq
タイトルCrystal structure of Zika NS3 protease with phenylacetyl-Lys-Lys-Arg-COOH inhibitor
要素
  • Serine protease NS3
  • Serine protease subunit NS2B
  • peptide PAC-DLY-DLY-DAR
キーワードHYDROLASE/HYDROLASE INHIBITOR / Viral protease / Serine protease / non-structural protein 3 / Zika protease / VIRAL PROTEIN / HYDROLASE-HYDROLASE 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 cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity ...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
Thrombin, subunit H - #120 / 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 ...Thrombin, subunit H - #120 / 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 / Trypsin-like serine proteases / Thrombin, subunit H / 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
N2-(phenylacetyl)-D-lysyl-D-lysyl-D-arginine / polypeptide(D) / 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: 1.987 Å
データ登録者Phoo, W.W. / Wirawan, M.
資金援助 シンガポール, ドイツ, 5件
組織認可番号国
start up grant シンガポール
CBRG15May045 シンガポール
NRF2016NRF-CRP001-063 シンガポール
Ministry of Education (Singapore)MOE2016-T2-2-097 シンガポール
DZIF-TTU 01.902 ドイツ
引用ジャーナル: Antiviral Res. / 年: 2018
タイトル: Structures of Zika virus NS2B-NS3 protease in complex with peptidomimetic inhibitors.
著者: Phoo, W.W. / Zhang, Z. / Wirawan, M. / Chew, E.J.C. / Chew, A.B.L. / Kouretova, J. / Steinmetzer, T. / Luo, D.
履歴
登録2018年4月5日登録サイト: PDBJ / 処理サイト: PDBJ
改定 1.02018年10月17日Provider: repository / タイプ: Initial release
改定 1.12018年10月31日Group: Data collection / Database references / カテゴリ: citation / citation_author
Item: _citation.journal_id_ISSN / _citation.journal_volume ..._citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
改定 1.22023年11月22日Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
改定 1.32024年10月23日Group: Structure summary
カテゴリ: pdbx_entry_details / pdbx_modification_feature

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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: Serine protease subunit NS2B
B: Serine protease NS3
C: Serine protease subunit NS2B
D: Serine protease NS3
E: Serine protease subunit NS2B
F: Serine protease NS3
G: Serine protease subunit NS2B
H: Serine protease NS3
I: peptide PAC-DLY-DLY-DAR
K: peptide PAC-DLY-DLY-DAR


分子量 (理論値)分子数
合計 (水以外)100,64710
ポリマ－100,64710
非ポリマー00
水8,989499
1
A: Serine protease subunit NS2B
B: Serine protease NS3


分子量 (理論値)分子数
合計 (水以外)24,8872
ポリマ－24,8872
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-26 kcal/mol
Surface area8950 Å2
手法PISA
2
C: Serine protease subunit NS2B
D: Serine protease NS3
I: peptide PAC-DLY-DLY-DAR


分子量 (理論値)分子数
合計 (水以外)25,4373
ポリマ－25,4373
非ポリマー00
水543
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area4850 Å2
ΔGint-22 kcal/mol
Surface area9090 Å2
手法PISA
3
E: Serine protease subunit NS2B
F: Serine protease NS3


分子量 (理論値)分子数
合計 (水以外)24,8872
ポリマ－24,8872
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-27 kcal/mol
Surface area8860 Å2
手法PISA
4
G: Serine protease subunit NS2B
H: Serine protease NS3
K: peptide PAC-DLY-DLY-DAR


分子量 (理論値)分子数
合計 (水以外)25,4373
ポリマ－25,4373
非ポリマー00
水543
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area4980 Å2
ΔGint-20 kcal/mol
Surface area9420 Å2
手法PISA
単位格子
Length a, b, c (Å)60.150, 60.330, 214.070
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
詳細The authors states the assemblies are heterodimers.

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要素

#1: タンパク質
Serine protease subunit NS2B


分子量: 5865.384 Da / 分子数: 4 / 由来タイプ: 組換発現 / 由来: (組換発現) Zika virus (ジカ熱ウイルス) / 株: Mr 766 / 発現宿主: Escherichia coli (大腸菌)
参照: UniProt: Q32ZE1, flavivirin, nucleoside-triphosphate phosphatase, RNA helicase
#2: タンパク質
Serine protease NS3


分子量: 19021.527 Da / 分子数: 4 / 由来タイプ: 組換発現
由来: (組換発現) Zika virus (strain Mr 766) (ジカ熱ウイルス)
株: Mr 766 / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: H8XX12, UniProt: Q32ZE1*PLUS
#3: Polypeptide(D) peptide PAC-DLY-DLY-DAR


タイプ: Peptide-like / クラス: 酵素阻害剤 / 分子量: 549.687 Da / 分子数: 2 / 由来タイプ: 合成 / 由来: (合成) synthetic construct (人工物) / 参照: N2-(phenylacetyl)-D-lysyl-D-lysyl-D-arginine
#4: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 499 / 由来タイプ: 天然 / 式: H2O
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: 1.93 Å3/Da / 溶媒含有率: 36.28 %
結晶化温度: 293.15 K / 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 4.6
詳細: 2 M ammonium sulfate, 0.1 M sodium acetate trihydrate pH 4.6

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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: 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6月12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
反射解像度: 1.987→60.33 Å / Num. obs: 53862 / % possible obs: 98.4 % / 冗長度: 5.6 % / CC1/2: 0.997 / Rmerge(I) obs: 0.107 / Rpim(I) all: 0.066 / Rrim(I) all: 0.117 / Net I/σ(I): 10.3
反射 シェル解像度: 1.987→2.04 Å / 冗長度: 5 % / Rmerge(I) obs: 0.486 / Mean I/σ(I) obs: 2.9 / Num. unique obs: 3829 / CC1/2: 0.796 / Rpim(I) all: 0.231 / Rrim(I) all: 0.541 / % possible all: 92.1

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解析

ソフトウェア
名称バージョン分類
PHENIX1.9_1692精密化
XDSデータ削減
SCALAデータスケーリング
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: 1.987→57.907 Å / 交差検証法: FREE R-VALUE / σ(F): 1.34 / 位相誤差: 28.85
Rfactor反射数%反射Selection details
Rfree0.2012 2649 4.93 %Random selection
Rwork0.1705 ---
obs0.175 53779 98.31 %-
溶媒の処理減衰半径: 0.9 Å / VDWプローブ半径: 1.11 Å
精密化ステップサイクル: LAST / 解像度: 1.987→57.907 Å
タンパク質核酸リガンド溶媒全体
原子数5688 0 0 499 6187
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.0035795
X-RAY DIFFRACTIONf_angle_d0.6857867
X-RAY DIFFRACTIONf_dihedral_angle_d11.9982007
X-RAY DIFFRACTIONf_chiral_restr0.027883
X-RAY DIFFRACTIONf_plane_restr0.0021014
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9894-2.02550.27661170.23562526X-RAY DIFFRACTION89
2.0255-2.06450.211130.23912531X-RAY DIFFRACTION90
2.0645-2.10660.24521380.2252542X-RAY DIFFRACTION89
2.1066-2.15240.28721360.22892570X-RAY DIFFRACTION90
2.1524-2.20250.24541350.21382580X-RAY DIFFRACTION92
2.2025-2.25750.23451390.20812650X-RAY DIFFRACTION93
2.2575-2.31860.27031460.20732683X-RAY DIFFRACTION94
2.3186-2.38680.2571280.20052672X-RAY DIFFRACTION95
2.3868-2.46380.2741290.21042693X-RAY DIFFRACTION95
2.4638-2.55180.26041250.20662720X-RAY DIFFRACTION95
2.5518-2.6540.2431420.20252715X-RAY DIFFRACTION95
2.654-2.77470.23181340.18632727X-RAY DIFFRACTION95
2.7747-2.92090.19811260.1862738X-RAY DIFFRACTION96
2.9209-3.10380.20361440.16362708X-RAY DIFFRACTION95
3.1038-3.34330.19751660.15672749X-RAY DIFFRACTION94
3.3433-3.67940.16761530.15062713X-RAY DIFFRACTION95
3.6794-4.21110.16511510.1382784X-RAY DIFFRACTION95
4.2111-5.30250.16561590.11922796X-RAY DIFFRACTION95
5.3025-34.92070.17211280.16252982X-RAY DIFFRACTION96
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)
11.85611.0611-0.48393.678-1.56942.38370.02570.13950.0607-0.11090.0893-0.1414-0.15650.13550.00570.18110.04540.01270.2548-0.06840.1615-21.180819.8742-7.8053
20.1067-0.0773-0.31750.05650.28133.24270.0264-0.29820.19870.15840.0054-0.0439-0.27070.1351-0.04720.3335-0.0118-0.01610.38640.07570.1872-34.259710.40464.5241
30.36120.0329-0.01390.4422-0.18760.69850.0399-0.0479-0.00870.01380.00310.2032-0.0893-0.0470.04010.26850.06970.01240.35410.01880.0103-47.771823.025-10.8916
40.93680.23210.11642.5650.26940.83630.0272-0.0465-0.0059-0.2170.055-0.2366-0.09710.2844-0.00540.2624-0.02460.02430.3292-0.05430.1034-20.782320.7226-8.7105
50.907-0.38430.06160.77850.04631.01610.045-0.09230.0846-0.24920.013-0.0767-0.05570.1792-0.01760.18240.01130.00310.2147-0.00330.055-27.829319.3614-13.5925
60.5796-0.21250.02380.59950.33671.13970.1233-0.08980.1555-0.00950.0706-0.0795-0.06430.21190.01530.3011-0.03490.08160.4514-0.01420.0481-22.641219.548-20.6645
70.2009-0.0782-0.12080.1482-0.02050.19590.03040.0389-0.0197-0.0396-0.02480.0223-0.0073-0.0523-0.02910.24630.0953-0.10980.28560.02-0.1327-33.56919.4421-20.5525
81.31910.0428-1.09590.2707-0.07791.0041-0.02170.0077-0.171-0.112-0.02860.11830.25680.05250.06340.225-0.006-0.03420.20620.00470.1724-38.05919.2278-11.5544
91.59051.3715-0.34511.992-0.17740.1287-0.0246-0.20150.08850.22060.0867-0.05190.00330.0706-0.01660.2150.01330.00180.232-0.05280.0792-31.160820.37350.3599
100.9178-0.32930.20940.6108-0.48051.138-0.0508-0.0633-0.1338-0.01440.00470.010.0511-0.0686-0.00370.1998-0.0130.01920.2421-0.00150.0678-44.802417.1503-4.1174
110.5161-0.0678-0.10780.5486-0.01610.338-0.09430.07120.0153-0.12440.02590.0403-0.0813-0.09040.02670.184-0.01670.00740.23-0.04680.0918-41.73221.5579-8.8839
122.37220.3735-0.67023.3479-1.21861.84850.0322-0.0892-0.30120.02920.01370.09820.2616-0.11660.01790.1818-0.0175-0.03230.24580.04090.1459-36.82668.6222-4.2767
130.62930.12040.53781.2758-0.73791.0247-0.0281-0.03550.0237-0.00650.07740.0167-0.0378-0.13180.01420.1833-0.01670.00890.2133-0.00820.046-40.879121.611-9.8198
140.86090.53450.25480.7642-0.11291.3788-0.06130.01910.0471-0.10620.02250.03580.01460.0040.00020.1752-0.0003-0.0040.2121-0.00330.1027-42.004820.893-10.6742
152.98020.49772.16620.29560.54262.59290.08230.04820.04380.0563-0.0164-0.07010.0160.0257-0.00310.3510.04360.03060.2865-0.01870.133-25.077532.5547-41.0035
160.03360.27310.17622.31351.47640.94410.07540.16960.0366-0.11790.0950.0471-0.1593-0.068-0.07490.3023-0.0024-0.00980.37460.04250.1239-34.15422.3789-56.3558
170.2913-0.00210.35580.6311-0.28140.97680.09760.0243-0.1422-0.03080.1516-0.13790.1367-0.01730.02990.33180.10780.030.3204-0.02010.1359-22.67254.1189-43.0671
180.2333-0.2976-0.23290.47120.20540.30930.0226-0.07680.3842-0.09490.05490.1223-0.17280.09770.00230.3350.0340.04750.2630.02330.1954-30.868832.4341-42.437
191.1373-0.3616-0.55630.67250.03670.5234-0.0133-0.0605-0.0426-0.08270.0405-0.0034-0.1188-0.0096-0.02670.26380.03650.00750.2377-0.02580.0786-28.738823.468-38.5123
201.6231-0.183-0.49030.9040.03280.77250.13730.02170.2451-0.07470.0632-0.0885-0.33730.1049-0.01660.3696-0.00820.04270.3536-0.0510.0524-29.291827.5774-30.8224
210.3859-0.2764-0.08150.3980.31020.5335-0.01920.0054-0.0763-0.022-0.00250.07360.0426-0.02390.00360.22920.01830.03120.23010.0030.0931-28.688313.373-45.6253
223.2555-0.32970.79782.23320.12431.52450.00040.05820.1053-0.06920.02390.1259-0.0727-0.12760.02050.25310.04880.00730.3075-0.02470.1552-9.369628.5742-66.2182
230.95221.0314-0.05321.70261.00372.20640.03140.0344-0.02220.05240.0785-0.11930.07520.0877-0.01490.2683-0.0591-0.00750.2785-0.00490.0771.521624.2642-56.6974
240.6781-0.32730.62531.41520.10360.80960.017-0.0919-0.01250.14490.0440.0365-0.0689-0.0230.01790.3933-0.0801-0.08280.42460.03130.15594.171914.3733-48.3862
250.32840.3030.45261.5391.54132.45260.0605-0.05-0.01920.0746-0.02670.05550.06870.08140.01320.38440.04240.05850.31830.05270.1017-4.70090.7794-52.7655
260.6944-0.11490.11290.9547-0.23290.6729-0.01390.1162-0.0242-0.11140.06540.02520.06010.00620.02570.3878-0.1087-0.03710.42590.02560.0621-9.6101-0.5747-72.3166
271.942-0.35920.34490.9926-0.09261.06070.04260.16940.23070.0930.07630.1372-0.28120.0587-0.00760.2508-0.01890.01970.20240.00110.1343-4.797226.4942-63.0125
280.1090.0955-0.08860.61180.06890.66160.0070.08770.0591-0.0231-0.00860.0691-0.1325-0.1165-0.01790.2458-0.00420.02550.22820.01160.0827-7.312121.9253-67.0085
290.6222-0.32540.18831.17950.56871.45360.112-0.02040.2589-0.07280.06140.0364-0.17380.0573-0.01540.35970.01550.0210.2698-0.0110.1456-7.273827.4401-72.2107
300.95330.164-0.54860.2030.30021.49380.115-0.08760.0950.0418-0.00830.0081-0.1702-0.07370.00620.3098-0.0730.04810.3365-0.0079-0.0507-1.157821.9291-76.6296
310.07040.1379-0.150.4727-0.52880.5859-0.02550.0336-0.0909-0.0535-0.0119-0.15870.0110.10920.02650.2075-0.01570.01340.2517-0.01560.07772.654511.676-68.7392
321.7853-1.26860.4271.6382-0.3710.1310.0475-0.12150.06930.26650.17020.0758-0.01590.0040.00140.2855-0.0110.02520.30230.0110.0884-4.757615.9585-53.2119
330.994-0.09580.23491.50440.76711.7161-0.0345-0.0576-0.17580.06870.0458-0.029-0.01480.064-0.04130.22440.02520.02620.22850.01450.0731-2.15893.9124-56.6529
340.57410.29080.150.4129-0.30360.7885-0.0150.1147-0.0907-0.12180.0830.0054-0.06120.06760.01630.28070.00370.01770.2551-0.00460.091-6.32895.7443-62.1064
355.3948-0.48911.93212.2174-0.60551.7166-0.0678-0.0764-0.10410.1858-0.121-0.44440.05570.27030.0120.23460.0356-0.0210.23660.0360.12375.294412.0433-57.3855
360.9599-0.36550.22091.19910.2341.19460.03120.0279-0.12270.0222-0.00570.13520.1438-0.0469-0.01250.21420.00020.01180.28460.0337-0.0182-6.61366.0049-62.877
371.4604-0.14110.18890.44540.39031.26750.06460.11740.0847-0.08720.1395-0.1835-0.12480.1792-0.0250.23660.00910.00120.3072-0.05040.150813.8749-11.6358-9.3315
384.9669-0.2975-4.15230.748-1.16466.237-0.0036-0.31890.23490.16730.0832-0.1173-0.35670.3562-0.07040.3631-0.0086-0.03250.30150.02110.21561.4305-20.27745.1873
390.7339-0.0154-0.03170.7934-0.47911.74050.0955-0.06880.057-0.0408-0.07880.13950.0044-0.16630.03240.28710.06510.01140.3203-0.05720.0911-12.7523-6.9544-9.877
400.8784-0.3653-0.45810.15190.190.2412-0.0244-0.07530.22520.0527-0.0596-0.0371-0.2316-0.09270.01620.25920.02480.00490.26780.00490.164819.1228-27.3752-10.5739
410.5278-0.1319-0.2490.03350.07740.60760.0811-0.05310.2099-0.02180.0439-0.1792-0.24520.1983-0.01620.2257-0.0231-0.0220.2724-0.08320.170213.3338-5.9953-9.8779
420.5872-0.39360.06140.77410.29710.67270.0535-0.09090.0302-0.04850.0539-0.0378-0.01280.1101-0.02320.20850.03840.02410.2404-0.010.02236.532-12.9329-14.4586
432.1935-0.6160.05421.30230.46330.82630.02220.0468-0.0139-0.06360.1027-0.12560.04270.0892-0.03690.3591-0.09850.03790.3783-0.08860.184314.1504-10.9708-20.9801
440.3748-0.0213-0.07420.2519-0.0670.17080.0430.0651-0.2209-0.0478-0.14780.0693-0.0269-0.0834-0.01020.260.0143-0.00750.22420.00020.0528-1.0226-17.9919-16.1571
451.78881.1079-0.2092.6473-0.12120.1940.028-0.09960.07730.2048-0.0022-0.21330.02570.1318-0.02920.20810.0495-0.01750.3107-0.0576-0.02854.6321-10.1009-0.1585
460.61980.0698-0.20510.82420.03470.69280.0318-0.0086-0.0418-0.0327-0.06080.0520.0615-0.15170.01920.19470.0024-0.01020.2435-0.04290.0963-7.3108-10.5363-5.5851
472.3494-0.1374-0.94222.8623-1.28132.4648-0.0647-0.1211-0.38760.0257-0.10250.14590.2667-0.19590.03650.2242-0.01190.01270.2213-0.0170.1243-1.6388-22.0202-3.3795
480.5013-0.1884-0.01741.00890.11650.4328-0.03950.0442-0.0032-0.0823-0.01970.0933-0.0373-0.04420.02860.1880.0042-0.00630.2104-0.02060.0536-6.4465-9.3675-9.3693
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 50 through 59 )
2X-RAY DIFFRACTION2chain 'A' and (resid 60 through 64 )
3X-RAY DIFFRACTION3chain 'A' and (resid 65 through 87 )
4X-RAY DIFFRACTION4chain 'B' and (resid 16 through 33 )
5X-RAY DIFFRACTION5chain 'B' and (resid 34 through 53 )
6X-RAY DIFFRACTION6chain 'B' and (resid 54 through 71 )
7X-RAY DIFFRACTION7chain 'B' and (resid 72 through 79 )
8X-RAY DIFFRACTION8chain 'B' and (resid 80 through 94 )
9X-RAY DIFFRACTION9chain 'B' and (resid 95 through 106 )
10X-RAY DIFFRACTION10chain 'B' and (resid 107 through 118 )
11X-RAY DIFFRACTION11chain 'B' and (resid 119 through 137 )
12X-RAY DIFFRACTION12chain 'B' and (resid 138 through 145 )
13X-RAY DIFFRACTION13chain 'B' and (resid 146 through 156 )
14X-RAY DIFFRACTION14chain 'B' and (resid 157 through 170 )
15X-RAY DIFFRACTION15chain 'C' and (resid 51 through 55 )
16X-RAY DIFFRACTION16chain 'C' and (resid 56 through 65 )
17X-RAY DIFFRACTION17chain 'C' and (resid 66 through 87 )
18X-RAY DIFFRACTION18chain 'D' and (resid 13 through 34 )
19X-RAY DIFFRACTION19chain 'D' and (resid 35 through 53 )
20X-RAY DIFFRACTION20chain 'D' and (resid 54 through 71 )
21X-RAY DIFFRACTION21chain 'D' and (resid 72 through 170 )
22X-RAY DIFFRACTION22chain 'E' and (resid 50 through 54 )
23X-RAY DIFFRACTION23chain 'E' and (resid 55 through 59 )
24X-RAY DIFFRACTION24chain 'E' and (resid 60 through 64 )
25X-RAY DIFFRACTION25chain 'E' and (resid 65 through 74 )
26X-RAY DIFFRACTION26chain 'E' and (resid 75 through 87 )
27X-RAY DIFFRACTION27chain 'F' and (resid 18 through 28 )
28X-RAY DIFFRACTION28chain 'F' and (resid 29 through 53 )
29X-RAY DIFFRACTION29chain 'F' and (resid 54 through 62 )
30X-RAY DIFFRACTION30chain 'F' and (resid 63 through 71 )
31X-RAY DIFFRACTION31chain 'F' and (resid 72 through 93 )
32X-RAY DIFFRACTION32chain 'F' and (resid 94 through 106 )
33X-RAY DIFFRACTION33chain 'F' and (resid 107 through 118 )
34X-RAY DIFFRACTION34chain 'F' and (resid 119 through 136 )
35X-RAY DIFFRACTION35chain 'F' and (resid 137 through 145 )
36X-RAY DIFFRACTION36chain 'F' and (resid 146 through 168 )
37X-RAY DIFFRACTION37chain 'G' and (resid 50 through 59 )
38X-RAY DIFFRACTION38chain 'G' and (resid 60 through 64 )
39X-RAY DIFFRACTION39chain 'G' and (resid 65 through 88 )
40X-RAY DIFFRACTION40chain 'H' and (resid 12 through 20 )
41X-RAY DIFFRACTION41chain 'H' and (resid 21 through 34 )
42X-RAY DIFFRACTION42chain 'H' and (resid 35 through 53 )
43X-RAY DIFFRACTION43chain 'H' and (resid 54 through 66 )
44X-RAY DIFFRACTION44chain 'H' and (resid 67 through 94 )
45X-RAY DIFFRACTION45chain 'H' and (resid 95 through 106 )
46X-RAY DIFFRACTION46chain 'H' and (resid 107 through 137 )
47X-RAY DIFFRACTION47chain 'H' and (resid 138 through 145 )
48X-RAY DIFFRACTION48chain 'H' and (resid 146 through 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