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COVID-19特輯

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冠狀病毒
冠狀病毒,2020. 由David S. Goodsell @ RCSB PDB原圖修改

最近爆發的新型冠狀病毒傳染病(Novel Coronavirus disease 2019: COVID-19)對全世界的人們都構成了嚴重威脅。 為了儘早了解新病毒(Severe Acute Respiratory Syndrome Coronavirus 2: SARS-CoV-2)以開發出有效的抗病毒藥物,已經有很多科研人員開始了相關蛋白結構的研究,並且將所獲得結構數據存儲與PDB。 PDBj為用戶提供了COVID-19相關數據一覽的門戶頁面,並將於每週三更新當日新發佈的相關數據。

有關該病毒蛋白質的解說,請參見下面的“當月的分子”頁面。

“所有結構”標籤的頁面則逐一羅列了所有的數據,包括由同一研究組提交的系列數據群。 “代表性結構”標籤的頁面精選具有相同胺基酸序列的結構數據中的高分辨率數據,不重複選擇具有同一胺基酸序列的數據,即使該數據可能包含不同的配體。 “最新條目”標籤內包含本週新更新數據。


Created: 2020-09-03 (last edited: more than 1 year ago)2022-09-02
9BO6
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BU of 9bo6 by Molmil
Crystal Structure of A173V/L50F SARS-CoV-2 Main Protease in Complex with Nirmatrelvir
Descriptor: (1R,2S,5S)-N-{(1E,2S)-1-imino-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-6,6-dimethyl-3-[3-methyl-N-(trifluoroacetyl)-L-valyl]-3-azabicyclo[3.1.0]hexane-2-carboxamide, 3C-like proteinase nsp5
Authors:Papini, C, Kenneson, J, Anderson, K.S.
Deposit date:2024-05-03
Release date:2025-02-12
Last modified:2025-03-12
Method:X-RAY DIFFRACTION (1.61 Å)
Cite:Exploring Possible Drug-Resistant Variants of SARS-CoV-2 Main Protease (M pro ) with Noncovalent Preclinical Candidate, Mpro61.
Acs Bio Med Chem Au, 5, 2025
9BO7
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BU of 9bo7 by Molmil
Crystal Structure of L50F SARS-CoV-2 Main Protease in Complex with Nirmatrelvir
Descriptor: (1R,2S,5S)-N-{(1E,2S)-1-imino-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-6,6-dimethyl-3-[3-methyl-N-(trifluoroacetyl)-L-valyl]-3-azabicyclo[3.1.0]hexane-2-carboxamide, 3C-like proteinase nsp5
Authors:Papini, C, Kenneson, J, Anderson, K.S.
Deposit date:2024-05-03
Release date:2025-02-12
Last modified:2025-03-12
Method:X-RAY DIFFRACTION (1.54 Å)
Cite:Exploring Possible Drug-Resistant Variants of SARS-CoV-2 Main Protease (M pro ) with Noncovalent Preclinical Candidate, Mpro61.
Acs Bio Med Chem Au, 5, 2025
9BO8
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BU of 9bo8 by Molmil
Crystal Structure of T21I SARS-CoV-2 Main Protease in Complex with GC376
Descriptor: 3C-like proteinase, N~2~-[(benzyloxy)carbonyl]-N-{(2S)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-L-leucinamide
Authors:Papini, C, Anderson, K.S.
Deposit date:2024-05-03
Release date:2025-02-12
Last modified:2025-03-12
Method:X-RAY DIFFRACTION (1.49 Å)
Cite:Exploring Possible Drug-Resistant Variants of SARS-CoV-2 Main Protease (M pro ) with Noncovalent Preclinical Candidate, Mpro61.
Acs Bio Med Chem Au, 5, 2025
9BO9
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BU of 9bo9 by Molmil
Crystal Structure of T190I SARS-CoV-2 Main Protease in Complex with GC376
Descriptor: 3C-like proteinase nsp5, N~2~-[(benzyloxy)carbonyl]-N-{(2S)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-L-leucinamide
Authors:Papini, C, Anderson, K.S.
Deposit date:2024-05-03
Release date:2025-02-12
Last modified:2025-03-12
Method:X-RAY DIFFRACTION (1.98 Å)
Cite:Exploring Possible Drug-Resistant Variants of SARS-CoV-2 Main Protease (M pro ) with Noncovalent Preclinical Candidate, Mpro61.
Acs Bio Med Chem Au, 5, 2025
9BOA
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BU of 9boa by Molmil
Crystal Structure of A173V SARS-CoV-2 Main Protease in Complex with GC376
Descriptor: 3C-like proteinase nsp5, N~2~-[(benzyloxy)carbonyl]-N-{(2S)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-L-leucinamide
Authors:Papini, C, Kenneson, J, Anderson, K.S.
Deposit date:2024-05-03
Release date:2025-02-12
Last modified:2025-03-12
Method:X-RAY DIFFRACTION (1.7 Å)
Cite:Exploring Possible Drug-Resistant Variants of SARS-CoV-2 Main Protease (M pro ) with Noncovalent Preclinical Candidate, Mpro61.
Acs Bio Med Chem Au, 5, 2025
9BOB
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BU of 9bob by Molmil
Crystal Structure of A173V/L50F SARS-CoV-2 Main Protease in Complex with GC376
Descriptor: 3C-like proteinase nsp5, N~2~-[(benzyloxy)carbonyl]-N-{(2S)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-L-leucinamide
Authors:Papini, C, Kenneson, J, Anderson, K.S.
Deposit date:2024-05-03
Release date:2025-02-12
Last modified:2025-03-12
Method:X-RAY DIFFRACTION (1.87 Å)
Cite:Exploring Possible Drug-Resistant Variants of SARS-CoV-2 Main Protease (M pro ) with Noncovalent Preclinical Candidate, Mpro61.
Acs Bio Med Chem Au, 5, 2025
9BOC
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BU of 9boc by Molmil
Crystal Structure of L50F SARS-CoV-2 Main Protease in Complex with GC376
Descriptor: 3C-like proteinase nsp5, N~2~-[(benzyloxy)carbonyl]-N-{(2S)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-L-leucinamide
Authors:Papini, C, Kenneson, J, Anderson, K.S.
Deposit date:2024-05-03
Release date:2025-02-12
Last modified:2025-03-12
Method:X-RAY DIFFRACTION (1.68 Å)
Cite:Exploring Possible Drug-Resistant Variants of SARS-CoV-2 Main Protease (M pro ) with Noncovalent Preclinical Candidate, Mpro61.
Acs Bio Med Chem Au, 5, 2025
9BOD
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BU of 9bod by Molmil
Crystal Structure of E166V/L50F SARS-CoV-2 Main Protease in Complex with GC376
Descriptor: 3C-like proteinase nsp5, N~2~-[(benzyloxy)carbonyl]-N-{(2S)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-L-leucinamide
Authors:Papini, C, Kenneson, J, Anderson, K.S.
Deposit date:2024-05-03
Release date:2025-02-12
Last modified:2025-03-12
Method:X-RAY DIFFRACTION (1.91 Å)
Cite:Exploring Possible Drug-Resistant Variants of SARS-CoV-2 Main Protease (M pro ) with Noncovalent Preclinical Candidate, Mpro61.
Acs Bio Med Chem Au, 5, 2025
9BOE
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BU of 9boe by Molmil
Crystal Structure of E166V SARS-CoV-2 Main Protease in Complex with GC376
Descriptor: 3C-like proteinase nsp5, N~2~-[(benzyloxy)carbonyl]-N-{(2S)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-L-leucinamide
Authors:Papini, C, Kenneson, J, Anderson, K.S.
Deposit date:2024-05-03
Release date:2025-02-12
Last modified:2025-03-12
Method:X-RAY DIFFRACTION (2.02 Å)
Cite:Exploring Possible Drug-Resistant Variants of SARS-CoV-2 Main Protease (M pro ) with Noncovalent Preclinical Candidate, Mpro61.
Acs Bio Med Chem Au, 5, 2025
9EX8
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BU of 9ex8 by Molmil
Free form of a mutant of SARS-CoV-2 main protease Mpro.
Descriptor: Non-structural protein 7
Authors:Battistutta, R, Fornasier, E, Giachin, G.
Deposit date:2024-04-05
Release date:2025-02-12
Method:X-RAY DIFFRACTION (1.8 Å)
Cite:Allostery in homodimeric SARS-CoV-2 main protease.
Commun Biol, 7, 2024
9EXU
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BU of 9exu by Molmil
Complex of a mutant of the SARS-CoV-2 main protease Mpro with the nsp4/5 substrate peptide (cocrystallization).
Descriptor: Non-structural protein 7, THR-SER-ALA-VAL-LEU-GLN-SER-GLY-PHE-ARG-LYS
Authors:Battistutta, R, Fornasier, E, Giachin, G.
Deposit date:2024-04-08
Release date:2025-02-12
Method:X-RAY DIFFRACTION (1.78 Å)
Cite:Allostery in homodimeric SARS-CoV-2 main protease.
Commun Biol, 7, 2024
9EYA
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BU of 9eya by Molmil
Complex of a mutant of the SARS-CoV-2 main protease Mpro with the nsp4/5 substrate peptide (soaking).
Descriptor: Non-structural protein 7, THR-SER-ALA-VAL-LEU-GLN-SER-GLY-PHE-ARG-LYS
Authors:Battistutta, R, Fornasier, E, Giachin, G.
Deposit date:2024-04-09
Release date:2025-02-12
Method:X-RAY DIFFRACTION (1.7 Å)
Cite:Allostery in homodimeric SARS-CoV-2 main protease.
Commun Biol, 7, 2024
9EZ4
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BU of 9ez4 by Molmil
Complex of a mutant of the SARS-CoV-2 main protease Mpro with the nsp5/6 substrate peptide.
Descriptor: 1,2-ETHANEDIOL, DI(HYDROXYETHYL)ETHER, GLUTAMINE, ...
Authors:Battistutta, R, Fornasier, E, Giachin, G.
Deposit date:2024-04-10
Release date:2025-02-12
Method:X-RAY DIFFRACTION (1.8 Å)
Cite:Allostery in homodimeric SARS-CoV-2 main protease.
Commun Biol, 7, 2024
9EZ6
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BU of 9ez6 by Molmil
Complex of a mutant of the SARS-CoV-2 main protease Mpro with the nsp14/15 substrate peptide.
Descriptor: 1,2-ETHANEDIOL, DI(HYDROXYETHYL)ETHER, DIMETHYL SULFOXIDE, ...
Authors:Battistutta, R, Fornasier, E, Giachin, G.
Deposit date:2024-04-10
Release date:2025-02-12
Method:X-RAY DIFFRACTION (1.87 Å)
Cite:Allostery in homodimeric SARS-CoV-2 main protease.
Commun Biol, 7, 2024
9J19
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BU of 9j19 by Molmil
The crystal structure of COVID-19 main protease in complex with an inhibitor minocycline
Descriptor: (4S,4AS,5AR,12AS)-4,7-BIS(DIMETHYLAMINO)-3,10,12,12A-TETRAHYDROXY-1,11-DIOXO-1,4,4A,5,5A,6,11,12A-OCTAHYDROTETRACENE-2- CARBOXAMIDE, 3C-like proteinase nsp5
Authors:Singh, A, Jangid, K, Dhaka, P, Tomar, S, Kumar, P.
Deposit date:2024-08-04
Release date:2025-02-12
Last modified:2025-04-09
Method:X-RAY DIFFRACTION (2.7 Å)
Cite:Structural and Mechanistic Insights into the Main Protease (Mpro) Dimer Interface Destabilization Inhibitor: Unveiling New Therapeutic Avenues against SARS-CoV-2.
Biochemistry, 64, 2025
9LAE
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BU of 9lae by Molmil
Locally refined region of SARS-CoV-2 spike in complex with antibodies 9G11 and 3E2.
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, Heavy chain of 3E2, Heavy chain of 9G11, ...
Authors:Jiang, Y, Sun, H, Zheng, Q, Li, S.
Deposit date:2025-01-02
Release date:2025-02-12
Last modified:2025-02-19
Method:ELECTRON MICROSCOPY (3.46 Å)
Cite:Structural insight into broadening SARS-CoV-2 neutralization by an antibody cocktail harbouring both NTD and RBD potent antibodies.
Emerg Microbes Infect, 13, 2024
8VYA
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BU of 8vya by Molmil
SARS-CoV-2 Omicron Variant Spike Glycoprotein Fusion Core (Q954H)
Descriptor: SARS-CoV-2 Omicron variant spike glycoprotein C-terminal heptad repeat domain, SARS-CoV-2 Omicron variant spike glycoprotein N-terminal heptad repeat domain (Q954H)
Authors:Outlaw, V.K, Apurba, R, Vithanage, N.
Deposit date:2024-02-07
Release date:2025-02-19
Method:X-RAY DIFFRACTION (2.12 Å)
Cite:SARS-CoV-2 Omicron Variant Spike Glycoprotein Mutation Q954H Enhances Fusion Core Stability
to be published
8Z46
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BU of 8z46 by Molmil
SARS-CoV-2 3CL protease (3CL pro) in complex with a novel inhibitor
Descriptor: (2~{S})-~{N}-(3-azanyl-3-oxidanylidene-propyl)-4-[4-[[(1~{S})-1-(2-chlorophenyl)-3-oxidanyl-propyl]amino]-6-(methylamino)-1,3,5-triazin-2-yl]-1-ethanoyl-piperazine-2-carboxamide, 3C-like proteinase nsp5
Authors:Zhao, W.F, Xiong, L.W, Xu, Y.C.
Deposit date:2024-04-16
Release date:2025-02-26
Method:X-RAY DIFFRACTION (1.57 Å)
Cite:Covalent DNA-Encoded Library Workflow Drives Discovery of SARS-CoV-2 Nonstructural Protein Inhibitors.
J.Am.Chem.Soc., 146, 2024
8Z4W
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BU of 8z4w by Molmil
Crystal structures of SARS-CoV-2 papain-like protease in complex with covalent inhibitors
Descriptor: 1-[4-[[[4-(isoquinolin-5-ylamino)-6-(methylamino)-1,3,5-triazin-2-yl]amino]methyl]piperidin-1-yl]ethanone, GLYCEROL, Non-structural protein 3, ...
Authors:Hu, H.C, Xu, Y.C.
Deposit date:2024-04-17
Release date:2025-02-26
Method:X-RAY DIFFRACTION (2.33 Å)
Cite:Covalent DNA-Encoded Library Workflow Drives Discovery of SARS-CoV-2 Nonstructural Protein Inhibitors.
J.Am.Chem.Soc., 146, 2024
9MZB
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BU of 9mzb by Molmil
X-ray crystallographic structure of Orf9b Apo Homodimer
Descriptor: GLYCINE, ORF9b protein
Authors:San Felipe, C.J, Fraser, J.S.
Deposit date:2025-01-22
Release date:2025-02-26
Method:X-RAY DIFFRACTION (2.8 Å)
Cite:X-ray Crystallographic Structure of Refolded Apo-Orf9b Homodimer
To Be Published
8W6W
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BU of 8w6w by Molmil
Crystal Structure of C-terminal domain of nucleocapsid protein from SARS-CoV-2 in complex with ampicillin
Descriptor: (2S,5R,6R)-6-{[(2R)-2-AMINO-2-PHENYLETHANOYL]AMINO}-3,3-DIMETHYL-7-OXO-4-THIA-1-AZABICYCLO[3.2.0]HEPTANE-2-CARBOXYLIC ACID, 1,2-ETHANEDIOL, Nucleoprotein
Authors:Dhaka, P, Mahto, J.K, Tomar, S, Kumar, P.
Deposit date:2023-08-30
Release date:2025-03-05
Last modified:2025-04-02
Method:X-RAY DIFFRACTION (2.2 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
9B0Y
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BU of 9b0y by Molmil
SARS CoV-2 Spike protein Ectodomain with internal tag, all RBD-down conformation
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:2024-03-12
Release date:2025-03-05
Last modified:2025-03-19
Method:ELECTRON MICROSCOPY (2.32 Å)
Cite:Production and cryo-electron microscopy structure of an internally tagged SARS-CoV-2 spike ecto-domain construct.
J Struct Biol X, 11, 2025
9B2V
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BU of 9b2v by Molmil
SARS CoV-2 Spike protein Ectodomain with internal tag, 1RBD-up conformation
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Spike glycoprotein, ...
Authors:Singh, S, Hasan, S.S.
Deposit date:2024-03-17
Release date:2025-03-05
Last modified:2025-03-19
Method:ELECTRON MICROSCOPY (2.55 Å)
Cite:Production and cryo-electron microscopy structure of an internally tagged SARS-CoV-2 spike ecto-domain construct.
J Struct Biol X, 11, 2025
9BJ2
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BU of 9bj2 by Molmil
Structure of the SARS-CoV-2 S 6P trimer complex with the human neutralizing antibody Fab fragment, C1533 (local refinement of NTD and C1533)
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, C1533 Heavy Chain, C1533 Light Chain, ...
Authors:Rubio, A.A, Abernathy, M.E, Barnes, C.O.
Deposit date:2024-04-24
Release date:2025-03-05
Last modified:2025-03-19
Method:ELECTRON MICROSCOPY (2.8 Å)
Cite:Bispecific antibodies targeting the N-terminal and receptor binding domains potently neutralize SARS-CoV-2 variants of concern.
Sci Transl Med, 17, 2025
9BJ3
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BU of 9bj3 by Molmil
Structure of the SARS-CoV-2 S 6P trimer complex with the human neutralizing antibody Fab fragment, C1596
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, C1596 Fab Heavy Chain, ...
Authors:Rubio, A.A, Abernathy, M.E, Barnes, C.O.
Deposit date:2024-04-24
Release date:2025-03-05
Last modified:2025-03-19
Method:ELECTRON MICROSCOPY (3.04 Å)
Cite:Bispecific antibodies targeting the N-terminal and receptor binding domains potently neutralize SARS-CoV-2 variants of concern.
Sci Transl Med, 17, 2025

238582

數據於2025-07-09公開中

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