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COVID-19特辑

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冠状病毒
冠状病毒,2020. 由David S. Goodsell @ RCSB PDB原图修改

最近爆发的新型冠状病毒传染病(Novel Coronavirus disease 2019: COVID-19)对全世界的人们都构成了严重威胁。 为了尽早了解新病毒(Severe Acute Respiratory Syndrome Coronavirus 2: SARS-CoV-2)以开发出有效的抗病毒药物,已经有很多科研人員开始了相关蛋白结构的研究,并且将所获得的结构数据存储于PDB。 PDBj为用户提供了COVID-19相关数据一览的门户页面,并将于每周三更新当日新发布的相关数据。

有关该病毒蛋白质的解说,请参见下面的“当月的分子”页面。

“所有结构”标签的页面则逐一罗列了所有的结构数据,包括由同一研究组提交的系列数据群。 “代表性结构”标签的页面精选具有相同氨基酸序列的结构数据中的高分辨率数据,不重复选择具同一氨基酸序列的数据,即使该数据可能包含不同配体。 “最新条目”标签内包含本周新更新数据。


Created: 2020-09-03 (last edited: more than 1 year ago)2020-12-02
9IN1
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BU of 9in1 by Molmil
Crystal Structure of C-terminal domain of nucleocapsid protein from SARS-CoV-2
Descriptor: Nucleoprotein
Authors:Dhaka, P, Mahto, J.K, Tomar, S, Kumar, P.
Deposit date:2024-07-05
Release date:2025-04-02
Method:X-RAY DIFFRACTION (1.4 Å)
Cite:Structural insights into the RNA binding inhibitors of the C-terminal domain of the SARS-CoV-2 nucleocapsid.
J.Struct.Biol., 217, 2025
9KSH
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BU of 9ksh by Molmil
Crystal structure of SARS-CoV-2 main protease in complex with compound 1
Descriptor: 3C-like proteinase nsp5, 6-[(6-chloranyl-2-methyl-indazol-5-yl)amino]-3-pyridin-3-yl-1-[[2,4,5-tris(fluoranyl)phenyl]methyl]-1,3,5-triazine-2,4-dione
Authors:Zhong, Y, Zhao, L, Zhang, W, Peng, W.
Deposit date:2024-11-29
Release date:2025-04-02
Method:X-RAY DIFFRACTION (1.91 Å)
Cite:Expanding the utilization of binding pockets proves to be effective for noncovalent small molecule inhibitors against SARS-CoV-2 M pro.
Eur.J.Med.Chem., 289, 2025
9KSJ
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BU of 9ksj by Molmil
Crystal structure of SARS-CoV-2 main protease in complex with compound 8
Descriptor: 3-[[(6E)-6-(6-chloranyl-2-methyl-indazol-5-yl)imino-3-[5-(2-methoxyethoxy)pyridin-3-yl]-2,4-bis(oxidanylidene)-1,3,5-triazinan-1-yl]methyl]-4-methyl-benzenecarbonitrile, 3C-like proteinase nsp5
Authors:Zhong, Y, Zhao, L, Zhang, W, Peng, W.
Deposit date:2024-11-29
Release date:2025-04-02
Method:X-RAY DIFFRACTION (1.67 Å)
Cite:Expanding the utilization of binding pockets proves to be effective for noncovalent small molecule inhibitors against SARS-CoV-2 M pro.
Eur.J.Med.Chem., 289, 2025
9LBS
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BU of 9lbs by Molmil
Cryo-EM structure of Omicron BA.1 RBD complexed with ConBA-998,S309 and S304Fabs
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose, Heavy chain of ConBA-998, Heavy chain of S304 Fab, ...
Authors:Zhang, Z, Ju, B, Liu, C.
Deposit date:2025-01-03
Release date:2025-04-02
Method:ELECTRON MICROSCOPY (3.41 Å)
Cite:Cryo-EM structure of Omicron BA.1 RBD complexed with ConBA-998,S309 and S304Fabs
To Be Published
9LDS
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BU of 9lds by Molmil
Crystal structure of nanobody H145 bound to SARS-CoV-2 spike stem-helix
Descriptor: H145, Spike protein S2'
Authors:Lu, G.W, Guo, L.Y, Lin, S.
Deposit date:2025-01-06
Release date:2025-04-02
Last modified:2025-07-02
Method:X-RAY DIFFRACTION (1.6 Å)
Cite:Structural basis and mode of action for two broadly neutralizing nanobodies targeting the highly conserved spike stem-helix of sarbecoviruses including SARS-CoV-2 and its variants.
Plos Pathog., 21, 2025
9LYO
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BU of 9lyo by Molmil
Alpha SARS-CoV-2 spike protein in complex with REGN10987 Fab homologue.
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, REGN10987 Fab homologue (Heavy chain), ...
Authors:Kocharovskaya, M.V, Pichkur, E.B, Shenkarev, Z.O, Lyukmanova, E.N.
Deposit date:2025-02-20
Release date:2025-04-02
Method:ELECTRON MICROSCOPY (3.07 Å)
Cite:Structure and dynamics of Alpha B.1.1.7 SARS-CoV-2 S-protein in complex with Fab of neutralizing antibody REGN10987.
Biochem.Biophys.Res.Commun., 755, 2025
9LYP
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BU of 9lyp by Molmil
Alpha SARS-CoV-2 spike protein RBD-down in complex with REGN10987 Fab homologue (local refinement)
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, REGN10987 Fab homologue (Heavy chain), REGN10987 Fab homologue (Light chain), ...
Authors:Kocharovskaya, M.V, Pichkur, E.B, Shenkarev, Z.O, Lyukmanova, E.N.
Deposit date:2025-02-20
Release date:2025-04-02
Method:ELECTRON MICROSCOPY (3.6 Å)
Cite:Structure and dynamics of Alpha B.1.1.7 SARS-CoV-2 S-protein in complex with Fab of neutralizing antibody REGN10987.
Biochem.Biophys.Res.Commun., 755, 2025
8YWY
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BU of 8ywy by Molmil
Crystal structure of SARS-Cov-2 main protease E166N mutant in complex with Bofutrelvir
Descriptor: 3C-like proteinase nsp5, ~{N}-[(2~{S})-3-cyclohexyl-1-oxidanylidene-1-[[(2~{S})-1-oxidanylidene-3-[(3~{S})-2-oxidanylidenepyrrolidin-3-yl]propan-2-yl]amino]propan-2-yl]-1~{H}-indole-2-carboxamide
Authors:Zhou, X.L, Wang, W.W, Zhang, J, Li, J.
Deposit date:2024-04-01
Release date:2025-04-09
Method:X-RAY DIFFRACTION (1.95 Å)
Cite:Inhibitory efficacy and structural insights of Bofutrelvir against SARS-CoV-2 M pro mutants and MERS-CoV M pro.
Commun Biol, 8, 2025
8YWZ
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BU of 8ywz by Molmil
Crystal structure of SARS-Cov-2 main protease H163A mutant in complex with Bofutrelvir
Descriptor: 3C-like proteinase nsp5, ~{N}-[(2~{S})-3-cyclohexyl-1-oxidanylidene-1-[[(2~{S})-1-oxidanylidene-3-[(3~{S})-2-oxidanylidenepyrrolidin-3-yl]propan-2-yl]amino]propan-2-yl]-1~{H}-indole-2-carboxamide
Authors:Zou, X.F, Wang, W.W, Zhang, J, Li, J.
Deposit date:2024-04-01
Release date:2025-04-09
Method:X-RAY DIFFRACTION (1.91 Å)
Cite:Inhibitory efficacy and structural insights of Bofutrelvir against SARS-CoV-2 M pro mutants and MERS-CoV M pro.
Commun Biol, 8, 2025
9INL
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BU of 9inl by Molmil
Crystal structure of SARS-Cov-2 main protease E166R mutant in complex with Bofutrelvir
Descriptor: Replicase polyprotein 1a, ~{N}-[(2~{S})-3-cyclohexyl-1-oxidanylidene-1-[[(2~{S})-1-oxidanylidene-3-[(3~{S})-2-oxidanylidenepyrrolidin-3-yl]propan-2-yl]amino]propan-2-yl]-1~{H}-indole-2-carboxamide
Authors:Zhou, X.L, Li, J.
Deposit date:2024-07-08
Release date:2025-04-09
Method:X-RAY DIFFRACTION (2.04 Å)
Cite:Inhibitory efficacy and structural insights of Bofutrelvir against SARS-CoV-2 M pro mutants and MERS-CoV M pro.
Commun Biol, 8, 2025
9LUF
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BU of 9luf by Molmil
Crystal structure of SARS-Cov-2 main protease S144A mutant in complex with Bofutrelvir
Descriptor: ORF1a polyprotein, ~{N}-[(2~{S})-3-cyclohexyl-1-oxidanylidene-1-[[(2~{S})-1-oxidanylidene-3-[(3~{S})-2-oxidanylidenepyrrolidin-3-yl]propan-2-yl]amino]propan-2-yl]-1~{H}-indole-2-carboxamide
Authors:Zhou, X.L, Li, J.
Deposit date:2025-02-08
Release date:2025-04-09
Method:X-RAY DIFFRACTION (1.99 Å)
Cite:Inhibitory efficacy and structural insights of Bofutrelvir against SARS-CoV-2 M pro mutants and MERS-CoV M pro.
Commun Biol, 8, 2025
9LUG
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BU of 9lug by Molmil
Crystal structure of SARS-Cov-2 main protease E166V mutant in complex with Bofutrelvir
Descriptor: ORF1a polyprotein, ~{N}-[(2~{S})-3-cyclohexyl-1-oxidanylidene-1-[[(2~{S})-1-oxidanylidene-3-[(3~{S})-2-oxidanylidenepyrrolidin-3-yl]propan-2-yl]amino]propan-2-yl]-1~{H}-indole-2-carboxamide
Authors:Zhou, X.L, Li, J.
Deposit date:2025-02-08
Release date:2025-04-09
Method:X-RAY DIFFRACTION (2.13 Å)
Cite:Inhibitory efficacy and structural insights of Bofutrelvir against SARS-CoV-2 M pro mutants and MERS-CoV M pro.
Commun Biol, 8, 2025
9B4X
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BU of 9b4x by Molmil
SARS CoV-2 full-length spike protein with Lys1269Ala and His1271Ala substitutions in the coatomer binding motif, 1RBD-up conformation (SPIKE-AXA)
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, ...
Authors:Singh, S, Hasan, S.S.
Deposit date:2024-03-21
Release date:2025-04-16
Method:ELECTRON MICROSCOPY (3.33 Å)
Cite:Cryo-EM structure of SARS CoV-2 full-length spike with Lys1269Ala and His1271Ala substitutions in the coatomer binding motif, 1RBD-up conformation
To Be Published
9B9U
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BU of 9b9u by Molmil
SARS-CoV-2 full-length spike protein with His1271Lys substitution in the coatomer binding motif, 1RBD-up conformation (SPIKE-KXK)
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose, ...
Authors:Singh, S, Hasan, S.S.
Deposit date:2024-04-03
Release date:2025-04-16
Method:ELECTRON MICROSCOPY (2.86 Å)
Cite:SARS CoV-2 full-length spike protein with His1271Lys substitution in the coatomer binding motif, 1RBD-up conformation
To Be Published
9BD9
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BU of 9bd9 by Molmil
SARS CoV-2 full-length WT spike protein, 1RBD-up conformation (SPIKE-WT)
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose, ...
Authors:Singh, S, Hasan, S.S.
Deposit date:2024-04-11
Release date:2025-04-16
Method:ELECTRON MICROSCOPY (2.95 Å)
Cite:Structure of SARS CoV-2 full-length spike protein, 1RBD-up conformation
To Be Published
9DHY
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BU of 9dhy by Molmil
Structure of SARS-CoV-2 spike in complex with antibody Fab COVIC-154
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Antibody Fab COVIC-154 Heavy Chain, ...
Authors:Yu, X, Saphire, E.O.
Deposit date:2024-09-04
Release date:2025-04-16
Method:ELECTRON MICROSCOPY (2.7 Å)
Cite:A global collaboration for systematic analysis of broad-ranging antibodies against the SARS-CoV-2 spike protein.
Cell Rep, 44, 2025
8Z2E
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BU of 8z2e by Molmil
Crystal structure of nanobody Tnb04-1 with antibody 1F11 fab and SARS-CoV-2 RBD
Descriptor: 1F11-H, 1F11-L, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, ...
Authors:Wang, X.Q, Zhang, L.Q, Chen, J, Dong, H.D.
Deposit date:2024-04-12
Release date:2025-04-23
Method:X-RAY DIFFRACTION (2.3 Å)
Cite:Crystal structure of nanobody Tnb04-1 with antibody 1F11 fab and SARS-CoV-2 RBD
To Be Published
9BC1
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BU of 9bc1 by Molmil
SARS-CoV-2 Mpro in complex with peptide mimetic inhibitor
Descriptor: 3C-like proteinase nsp5, peptide mimetic inhibitor
Authors:Afsar, M, Priscila, B, Olsen, S.K.
Deposit date:2024-04-07
Release date:2025-04-23
Method:X-RAY DIFFRACTION (1.72 Å)
Cite:SARS-CoV-2 Mpro in complex with peptide mimetic inhibitor
To Be Published
9KN1
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BU of 9kn1 by Molmil
Crystal structure of SARS-CoV-2 nucleocapsid phosphoprotein N-terminal domain(N-NTD) in complex with UMP
Descriptor: Nucleoprotein, PHOSPHATE ION, URIDINE-5'-MONOPHOSPHATE
Authors:Higashiura, A, Yamamoto, A, Ito, H.
Deposit date:2024-11-18
Release date:2025-04-23
Method:X-RAY DIFFRACTION (2.12 Å)
Cite:Structural insights into nucleocapsid protein variability: Implications for PJ34 efficacy against SARS-CoV-2.
Virology, 604, 2025
8Z9L
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BU of 8z9l by Molmil
Crystal structure of SARS-CoV-2 RBD bound to Rhinolophus affinis ACE2
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, Angiotensin-converting enzyme, Spike protein S1, ...
Authors:Lan, J, Wang, C.H.
Deposit date:2024-04-23
Release date:2025-04-30
Last modified:2025-05-14
Method:X-RAY DIFFRACTION (3.598 Å)
Cite:Molecular mechanisms of RaTG13 and SARS-CoV-2 RBD bound to Rhinolophus affinis bat ACE2.
Protein Sci., 34, 2025
8ZBF
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BU of 8zbf by Molmil
Crystal structure of the A58-T10 DNA aptamer in complex with SARS-CoV-2 N-NTD
Descriptor: DNA (40-MER), Nucleoprotein, SODIUM ION
Authors:Chen, X, Huang, L.
Deposit date:2024-04-26
Release date:2025-04-30
Last modified:2025-05-07
Method:X-RAY DIFFRACTION (2.8 Å)
Cite:Molecular characterization and broad-spectrum mechanism of coronavirus N protein aptamer
To Be Published
9DU2
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BU of 9du2 by Molmil
SARS-CoV-2 Mpro in complex with compound 7
Descriptor: 3C-like proteinase nsp5, N-[(2S)-3-cyclopropyl-1-{[(1Z,2S)-1-imino-4-(methanesulfonyl)butan-2-yl]amino}-1-oxopropan-2-yl]-4-methoxy-1H-indole-2-carboxamide
Authors:Bigelow, L, Tang, H, Boguslaw, N, Duda, D.M.
Deposit date:2024-10-02
Release date:2025-04-30
Method:X-RAY DIFFRACTION (1.86 Å)
Cite:Inhibition of Dimeric SARS-CoV-2 Mpro by Aldehyde and Nitrilebased Inhibitors Displays Positive Cooperativity and a Mixture of Covalent and Non-covalent Binding.
To Be Published
9FM4
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BU of 9fm4 by Molmil
Dynamic structure of the apical stem loop of the stem loop 2 motif (s2m) from SCoV-2 Delta variant.
Descriptor: RNA (25-MER)
Authors:Wirtz Martin, M.A, Matzel, T, Makowski, J, Kensinger, A, Herr, A, Wacker, A, Richter, C, Jonker, H.R.A, Evanseck, J, Schwalbe, H.
Deposit date:2024-06-05
Release date:2025-05-07
Last modified:2025-06-04
Method:SOLUTION NMR, SOLUTION SCATTERING
Cite:Characterization of structure and dynamics of the apical stem loop of s2m from SCoV-2 Delta by NMR spectroscopy, validated by MD and SAXS
To Be Published
8X1X
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BU of 8x1x by Molmil
SARS-CoV-2 Papain like protease (PLpro) in complex with inhibitor Lithocholic acid
Descriptor: (3beta,5beta,14beta,17alpha)-3-hydroxycholan-24-oic acid, GLYCEROL, Papain-like protease nsp3, ...
Authors:Choudhary, S, Verma, S, Kumar, P, Tomar, S.
Deposit date:2023-11-09
Release date:2025-05-14
Method:X-RAY DIFFRACTION (2.3 Å)
Cite:SARS-CoV-2 Papain like protease (PLpro) in complex with inhibitor Lithocholic acid
To Be Published
9BLF
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BU of 9blf by Molmil
SARS-CoV-2 core polymerase complex inhibited by araCTP
Descriptor: 4-amino-1-{5-O-[(S)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]-beta-D-arabinofuranosyl}pyrimidin-2(1H)-one, MAGNESIUM ION, Non-structural protein 7, ...
Authors:Anderson, T.K, Kirchdeorfer, R.N.
Deposit date:2024-04-30
Release date:2025-05-14
Method:ELECTRON MICROSCOPY (3.31 Å)
Cite:Structure of the SARS-CoV-2 core-RTC bound to RNA, araCMP, and araCTP
To Be Published

238582

数据于2025-07-09公开中

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