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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
9J8T
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BU of 9j8t by Molmil
Crystal structure of SARS-CoV-2 main protease in complex with Mp-4L2
Descriptor: 3C-like proteinase nsp5, TYR-DSG-DLE-DPN-DGN-ARG-DTH-DAS-DTR-DTH-ALO-DGN-DTY-CCJ-GLY-NH2
Authors:Shi, Y.S, Yang, J.Y, Wang, M.W.
Deposit date:2024-08-21
Release date:2025-07-02
Method:X-RAY DIFFRACTION (2.39 Å)
Cite:De novo discovery of a non-covalent cell-penetrating bicyclic peptide inhibitor targeting SARS-CoV-2 main protease
To Be Published
9J8U
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BU of 9j8u by Molmil
Crystal structure of SARS-CoV-2 main protease in complex with Mp-4D7
Descriptor: 3C-like proteinase nsp5, DTY-VAL-THR-PHE-HIS-ALO-2TL-2TL-PRO-PHE-LEU-DPR-PRO-CCJ-GLY-NH2
Authors:Shi, Y.S, Yang, J.Y, Wang, M.W.
Deposit date:2024-08-21
Release date:2025-07-02
Method:X-RAY DIFFRACTION (2.71 Å)
Cite:De novo discovery of a non-covalent cell-penetrating bicyclic pep-tide inhibitor targeting SARS-CoV-2 main protease
To Be Published
9P6P
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BU of 9p6p by Molmil
Crystal Structure of the SARS-CoV-2 2'-O-Methyltransferase with (m7GpppA)pUpU (Cap-0) and S-Adenosyl-L-homocysteine (SAH).
Descriptor: 2'-O-methyltransferase, 7N-METHYL-8-HYDROGUANOSINE-5'-TRIPHOSPHATE, CHLORIDE ION, ...
Authors:Minasov, G, Shuvalova, L, Maltseva, N, Kim, Y, Kiryukhina, O, Joachimiak, A, Satchell, K.J.F, Center for Structural Biology of Infectious Diseases (CSBID)
Deposit date:2025-06-19
Release date:2025-07-02
Method:X-RAY DIFFRACTION (1.95 Å)
Cite:Crystal Structure of the SARS-CoV-2 2'-O-Methyltransferase with (m7GpppA)pUpU (Cap-0) and S-Adenosyl-L-homocysteine (SAH).
To Be Published
9CJO
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BU of 9cjo by Molmil
X-ray crystal structure of SARS-CoV-2 main protease quadruple mutants
Descriptor: 3C-like proteinase nsp5
Authors:Esler, M.A, Shi, K, Harris, R.S, Aihara, H.
Deposit date:2024-07-07
Release date:2025-07-09
Method:X-RAY DIFFRACTION (2.33 Å)
Cite:X-ray crystal structure of SARS-CoV-2 main protease quadruple mutants
To Be Published
9CJP
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BU of 9cjp by Molmil
X-ray crystal structure of SARS-CoV-2 main protease quadruple mutants 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, 1,2-ETHANEDIOL, 3C-like proteinase nsp5, ...
Authors:Esler, M.A, Shi, K, Harris, R.S, Aihara, H.
Deposit date:2024-07-07
Release date:2025-07-09
Method:X-RAY DIFFRACTION (1.71 Å)
Cite:X-ray crystal structure of SARS-CoV-2 main protease quadruple mutants in complex with Nirmatrelvir
To Be Published
9CJQ
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BU of 9cjq by Molmil
X-ray crystal structure of SARS-CoV-2 main protease quadruple mutants in complex with Ensitrelvir
Descriptor: 1,2-ETHANEDIOL, 6-[(6-chloranyl-2-methyl-indazol-5-yl)amino]-3-[(1-methyl-1,2,4-triazol-3-yl)methyl]-1-[[2,4,5-tris(fluoranyl)phenyl]methyl]-1,3,5-triazine-2,4-dione, main protease
Authors:Esler, M.A, Shi, K, Harris, R.S, Aihara, H.
Deposit date:2024-07-07
Release date:2025-07-09
Method:X-RAY DIFFRACTION (2.24 Å)
Cite:X-ray crystal structure of SARS-CoV-2 main protease quadruple mutants in complex with Ensitrelvir
To Be Published
9CJR
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BU of 9cjr by Molmil
X-ray crystal structure of SARS-CoV-2 main protease double mutants in complex with Ensitrelvir
Descriptor: 3C-like proteinase nsp5, 6-[(6-chloranyl-2-methyl-indazol-5-yl)amino]-3-[(1-methyl-1,2,4-triazol-3-yl)methyl]-1-[[2,4,5-tris(fluoranyl)phenyl]methyl]-1,3,5-triazine-2,4-dione, CHLORIDE ION, ...
Authors:Esler, M.A, Shi, K, Harris, R.S, Aihara, H.
Deposit date:2024-07-07
Release date:2025-07-09
Method:X-RAY DIFFRACTION (1.65 Å)
Cite:X-ray crystal structure of SARS-CoV-2 main protease double mutants in complex with Ensitrelvir
To Be Published
9CJS
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BU of 9cjs by Molmil
X-ray crystal structure of SARS-CoV-2 main protease triple mutants 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:Esler, M.A, Shi, K, Harris, R.S, Aihara, H.
Deposit date:2024-07-07
Release date:2025-07-09
Method:X-RAY DIFFRACTION (2.09 Å)
Cite:X-ray crystal structure of SARS-CoV-2 main protease triple mutants in complex with Bofutrelvir
To Be Published
9CJT
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BU of 9cjt by Molmil
X-ray crystal structure of SARS-CoV-2 main protease quadruple mutants 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:Esler, M.A, Shi, K, Harris, R.S, Aihara, H.
Deposit date:2024-07-07
Release date:2025-07-09
Method:X-RAY DIFFRACTION (1.92 Å)
Cite:X-ray crystal structure of SARS-CoV-2 main protease quadruple mutants in complex with Bofutrelvir
To Be Published
9CJU
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BU of 9cju by Molmil
Structure of SARS-CoV-2 main protease in complex with Bofutrelvir in orthorhombic form
Descriptor: 1,2-ETHANEDIOL, DI(HYDROXYETHYL)ETHER, Non-structural protein 7, ...
Authors:Esler, M.A, Shi, K, Harris, R.S, Aihara, H.
Deposit date:2024-07-07
Release date:2025-07-09
Method:X-RAY DIFFRACTION (1.68 Å)
Cite:To be published
To Be Published
9CJV
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BU of 9cjv by Molmil
X-ray crystal structure of SARS-CoV-2 main protease complex with Bofutrelvir
Descriptor: 3C-like proteinase nsp5, DIMETHYL SULFOXIDE, ~{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:Esler, M.A, Shi, K, Aihara, H.
Deposit date:2024-07-07
Release date:2025-07-09
Method:X-RAY DIFFRACTION (1.91 Å)
Cite:X-ray crystal structure of SARS-CoV-2 main protease complex with Bofutrelvir
To Be Published
9E9Q
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BU of 9e9q by Molmil
SARS-CoV-2 SL5 crystal structure native
Descriptor: MAGNESIUM ION, RNA (101-MER)
Authors:Jones, C.P, Ferre-D'Amare, A.R.
Deposit date:2024-11-08
Release date:2025-07-09
Method:X-RAY DIFFRACTION (3.33 Å)
Cite:Crystallographic and cryoEM analyses reveal SARS-CoV-2 SL5 is a mobile T-shaped four-way junction with deep pockets.
Rna, 31, 2025
9FWH
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BU of 9fwh by Molmil
Crystal Structure of SARS-CoV-2 NSP10-ExoN in complex with VT00019
Descriptor: (4R)-4-phenyl-1,2-thiazolidine 1,1-dioxide, Guanine-N7 methyltransferase nsp14, Non-structural protein 10, ...
Authors:Krojer, T, Kozielski, F, Sele, C, Nyblom, M, Fisher, S.Z, Knecht, W.
Deposit date:2024-06-30
Release date:2025-07-09
Method:X-RAY DIFFRACTION (2.35 Å)
Cite:Crystal Structure of SARS-CoV-2 NSP10-ExoN in complex with VT00019
To Be Published
9FWI
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BU of 9fwi by Molmil
Ensemble model of ligand-free SARS-CoV-2 NSP10-NSP14 (ExoN) and in complex with partially bound VT00025
Descriptor: (3-oxidanylazetidin-1-yl)-phenyl-methanone, DIMETHYL SULFOXIDE, Guanine-N7 methyltransferase nsp14, ...
Authors:Krojer, T, Kozielski, F, Sele, C, Nyblom, M, Fisher, S.Z, Knecht, W.
Deposit date:2024-06-30
Release date:2025-07-09
Method:X-RAY DIFFRACTION (1.533 Å)
Cite:Ensemble model of ligand-free SARS-CoV-2 NSP10-NSP14 (ExoN) and in complex with partially bound VT00025
To Be Published
9FWJ
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BU of 9fwj by Molmil
Ensemble model of ligand-free SARS-CoV-2 NSP10-NSP14 (ExoN) and in complex with partially bound VT00079
Descriptor: 2-methoxybenzamide, Guanine-N7 methyltransferase nsp14, MAGNESIUM ION, ...
Authors:Krojer, T, Kozielski, F, Sele, C, Nyblom, M, Fisher, S.Z, Knecht, W.
Deposit date:2024-06-30
Release date:2025-07-09
Method:X-RAY DIFFRACTION (2.424 Å)
Cite:Ensemble model of ligand-free SARS-CoV-2 NSP10-NSP14 (ExoN) and in complex with partially bound VT00079
To Be Published
9FWL
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BU of 9fwl by Molmil
Ensemble model of ligand-free SARS-CoV-2 NSP10-NSP14 (ExoN) and in complex with partially bound VT00025
Descriptor: 3-phenylthiophene-2-carboxamide, DIMETHYL SULFOXIDE, Guanine-N7 methyltransferase nsp14, ...
Authors:Krojer, T, Kozielski, F, Sele, C, Nyblom, M, Fisher, S.Z, Knecht, W.
Deposit date:2024-06-30
Release date:2025-07-09
Method:X-RAY DIFFRACTION (2.09 Å)
Cite:Ensemble model of ligand-free SARS-CoV-2 NSP10-NSP14 (ExoN) and in complex with partially bound VT00025
To Be Published
9FWM
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BU of 9fwm by Molmil
Crystal Structure of SARS-CoV-2 NSP10-NSP14 (ExoN) in complex with VT00180
Descriptor: 1H-indole-3-carboxamide, DIMETHYL SULFOXIDE, Guanine-N7 methyltransferase nsp14, ...
Authors:Krojer, T, Kozielski, F, Sele, C, Nyblom, M, Fisher, S.Z, Knecht, W.
Deposit date:2024-06-30
Release date:2025-07-09
Method:X-RAY DIFFRACTION (1.574 Å)
Cite:Crystal Structure of SARS-CoV-2 NSP10-NSP14 (ExoN) in complex with VT00180
To Be Published
9FWN
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BU of 9fwn by Molmil
Crystal Structure of SARS-CoV-2 NSP10-NSP14 (ExoN) in complex with VT00219
Descriptor: 1-methyl-1-(phenylmethyl)urea, DIMETHYL SULFOXIDE, Guanine-N7 methyltransferase nsp14, ...
Authors:Krojer, T, Kozielski, F, Sele, C, Nyblom, M, Fisher, S.Z, Knecht, W.
Deposit date:2024-06-30
Release date:2025-07-09
Method:X-RAY DIFFRACTION (1.866 Å)
Cite:Crystal Structure of SARS-CoV-2 NSP10-NSP14 (ExoN) in complex with VT00219
To Be Published
9FWO
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BU of 9fwo by Molmil
Crystal Structure of SARS-CoV-2 NSP10-NSP14 (ExoN) in complex with VT00216
Descriptor: 1-methylpyrrole-2-carboxamide, Guanine-N7 methyltransferase nsp14, MAGNESIUM ION, ...
Authors:Krojer, T, Kozielski, F, Sele, C, Nyblom, M, Fisher, S.Z, Knecht, W.
Deposit date:2024-06-30
Release date:2025-07-09
Method:X-RAY DIFFRACTION (2.179 Å)
Cite:Crystal Structure of SARS-CoV-2 NSP10-NSP14 (ExoN) in complex with VT00216
To Be Published
9FWP
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BU of 9fwp by Molmil
Crystal Structure of SARS-CoV-2 NSP10-NSP14 (ExoN) in complex with VT00198
Descriptor: Guanine-N7 methyltransferase nsp14, MAGNESIUM ION, N-methylbenzamide, ...
Authors:Krojer, T, Kozielski, F, Sele, C, Nyblom, M, Fisher, S.Z, Knecht, W.
Deposit date:2024-06-30
Release date:2025-07-09
Method:X-RAY DIFFRACTION (2.381 Å)
Cite:Crystal Structure of SARS-CoV-2 NSP10-NSP14 (ExoN) in complex with VT00198
To Be Published
9FWQ
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BU of 9fwq by Molmil
Crystal Structure of SARS-CoV-2 NSP10-NSP14 (ExoN) in complex with VT00218
Descriptor: 5,6,7,8-tetrahydro-[1,2,4]triazolo[4,3-a]pyridine, Guanine-N7 methyltransferase nsp14, MAGNESIUM ION, ...
Authors:Krojer, T, Kozielski, F, Sele, C, Nyblom, M, Fisher, S.Z, Knecht, W.
Deposit date:2024-06-30
Release date:2025-07-09
Method:X-RAY DIFFRACTION (2.322 Å)
Cite:Crystal Structure of SARS-CoV-2 NSP10-NSP14 (ExoN) in complex with VT00218
To Be Published
9FWR
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BU of 9fwr by Molmil
Crystal Structure of SARS-CoV-2 NSP10-NSP14 (ExoN) in complex with VT00249
Descriptor: (4R)-4-phenyl-1,3-oxazolidin-2-one, Guanine-N7 methyltransferase nsp14, MAGNESIUM ION, ...
Authors:Krojer, T, Kozielski, F, Sele, C, Nyblom, M, Fisher, S.Z, Knecht, W.
Deposit date:2024-06-30
Release date:2025-07-09
Method:X-RAY DIFFRACTION (2.294 Å)
Cite:Crystal Structure of SARS-CoV-2 NSP10-NSP14 (ExoN) in complex with VT00249
To Be Published
9FWS
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BU of 9fws by Molmil
Crystal Structure of SARS-CoV-2 NSP10-NSP14 (ExoN) in complex with VT00258
Descriptor: 7-METHOXY-1H-INDAZOLE, DIMETHYL SULFOXIDE, Guanine-N7 methyltransferase nsp14, ...
Authors:Krojer, T, Kozielski, F, Sele, C, Nyblom, M, Fisher, S.Z, Knecht, W.
Deposit date:2024-06-30
Release date:2025-07-09
Method:X-RAY DIFFRACTION (1.433 Å)
Cite:Crystal Structure of SARS-CoV-2 NSP10-NSP14 (ExoN) in complex with VT00258
To Be Published
9FWT
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BU of 9fwt by Molmil
Ensemble model of ligand-free SARS-CoV-2 NSP10-NSP14 (ExoN) and in complex with partially bound VT00259
Descriptor: DIMETHYL SULFOXIDE, Guanine-N7 methyltransferase nsp14, Non-structural protein 10, ...
Authors:Krojer, T, Kozielski, F, Sele, C, Nyblom, M, Fisher, S.Z, Knecht, W.
Deposit date:2024-06-30
Release date:2025-07-09
Method:X-RAY DIFFRACTION (1.639 Å)
Cite:Ensemble model of ligand-free SARS-CoV-2 NSP10-NSP14 (ExoN) and in complex with partially bound VT00259
To Be Published
9FWU
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BU of 9fwu by Molmil
Crystal Structure of SARS-CoV-2 NSP10-NSP14 (ExoN) in complex with VT00421
Descriptor: DIMETHYL SULFOXIDE, Guanine-N7 methyltransferase nsp14, N,N-dimethyl-3-oxidanyl-benzamide, ...
Authors:Krojer, T, Kozielski, F, Sele, C, Nyblom, M, Fisher, S.Z, Knecht, W.
Deposit date:2024-06-30
Release date:2025-07-09
Method:X-RAY DIFFRACTION (1.425 Å)
Cite:Crystal Structure of SARS-CoV-2 NSP10-NSP14 (ExoN) in complex with VT00421
To Be Published

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數據於2025-07-09公開中

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