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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
所有結構 (5197)代表性結構 (2266)最新條目 (44)
9ML8
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BU of 9ml8 by Molmil
Crystal structure of the SARS-CoV-2 RBD in complex with the rabbit M8b-B1 Fab
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, M8b-B1 heavy chain, M8b-B1 light chain, ...
Authors:Fan, C, Bjorkman, P.J.
Deposit date:2024-12-18
Release date:2025-06-04
Method:X-RAY DIFFRACTION (2.4 Å)
Cite:Cross-reactive sarbecovirus antibodies induced by mosaic RBD nanoparticles.
Proc.Natl.Acad.Sci.USA, 122, 2025
9ML9
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BU of 9ml9 by Molmil
Crystal structure of the SARS-CoV-2 RBD in complex with the rabbit M8b-C9 Fab
Descriptor: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL, 2-acetamido-2-deoxy-beta-D-glucopyranose, M8b-C9 heavy chain, ...
Authors:Fan, C, Bjorkman, P.J.
Deposit date:2024-12-18
Release date:2025-06-04
Method:X-RAY DIFFRACTION (2.59 Å)
Cite:Cross-reactive sarbecovirus antibodies induced by mosaic RBD nanoparticles.
Proc.Natl.Acad.Sci.USA, 122, 2025
9MRW
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BU of 9mrw by Molmil
Functional Implications of Hexameric Dynamics in SARS-CoV-2 Nsp15
Descriptor: Uridylate-specific endoribonuclease nsp15
Authors:Ketawala, G.K, Sonowal, M, Schrag, L, Fromme, R, Botha, S, Fromme, P.
Deposit date:2025-01-08
Release date:2025-06-04
Method:X-RAY DIFFRACTION (3 Å)
Cite:Functional implications of hexameric dynamics in SARS-CoV-2 Nsp15.
Protein Sci., 34, 2025
9MRY
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BU of 9mry by Molmil
Functional Implications of HexamericDynamics in SARS-CoV-2 Nsp15
Descriptor: Uridylate-specific endoribonuclease nsp15
Authors:Ketawala, G.K, Sonowal, M, Schrag, L, Fromme, R, Botha, S, Fromme, P.
Deposit date:2025-01-09
Release date:2025-06-04
Method:X-RAY DIFFRACTION (3 Å)
Cite:Functional implications of hexameric dynamics in SARS-CoV-2 Nsp15.
Protein Sci., 34, 2025
8XCH
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BU of 8xch by Molmil
SARS-CoV-2 Replication-Transcription Complex has a dimer-of-dimeric architecture (ddRTC) in pre-capping initiation.
Descriptor: ADENOSINE-5'-DIPHOSPHATE, Helicase, MAGNESIUM ION, ...
Authors:Yan, L, Lou, Z.
Deposit date:2023-12-09
Release date:2025-06-11
Method:ELECTRON MICROSCOPY (3.4 Å)
Cite:Structural basis for template-product RNA duplex unwinding by SARS-CoV-2 helicase
To Be Published
8ZPQ
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BU of 8zpq by Molmil
Crystal structure of SARS-Cov-2-BQ1.1-RBD and 70fab
Descriptor: 70fab-H, 70fab-L, Spike protein S1
Authors:Wu, Y, Gao, F.
Deposit date:2024-05-31
Release date:2025-06-11
Method:X-RAY DIFFRACTION (2.75 Å)
Cite:Crystal structure of SARS-Cov-2-BQ1.1-RBD and 70fab
To Be Published
8ZQ8
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BU of 8zq8 by Molmil
SARS-Cov-2 3CL protease in complex with macrocyclic inhibitor CG-1039
Descriptor: 3C-like proteinase nsp5, CG-1039
Authors:Chen, X, Hou, K, Tang, X.
Deposit date:2024-06-01
Release date:2025-06-11
Method:X-RAY DIFFRACTION (1.77 Å)
Cite:SARS-Cov-2 3CL protease in complex with macrocyclic inhibitor CG-1039
To Be Published
8ZT9
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BU of 8zt9 by Molmil
The Crystal structure of mol066 bound to the main protease (3CLpro/Mpro) of SARS-CoV-2
Descriptor: 3C-like proteinase, 6-[(6-chloranyl-2-propan-2-yl-indazol-5-yl)amino]-3-[(1-methyl-1,2,4-triazol-3-yl)methyl]-1-[[2,4,5-tris(fluoranyl)phenyl]methyl]pyrimidine-2,4-dione, GLYCEROL
Authors:Yan, M, Zhang, H.
Deposit date:2024-06-06
Release date:2025-06-11
Method:X-RAY DIFFRACTION (1.8 Å)
Cite:Development of pyrimidone derivatives as nonpeptidic and noncovalent 3-chymotrypsin-like protease (3CL pro ) inhibitors with anti-coronavirus activities.
Bioorg.Chem., 154, 2025
8ZUC
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BU of 8zuc by Molmil
The Crystal structure of mol080 bound to the main protease (3CLpro/Mpro) of SARS-CoV-2
Descriptor: 3C-like proteinase, 6-[[6-chloranyl-2-(3-methylbutyl)indazol-5-yl]amino]-3-[(1-methyl-1,2,4-triazol-3-yl)methyl]-1-[[2,4,5-tris(fluoranyl)phenyl]methyl]pyrimidine-2,4-dione
Authors:Yan, M, Zhang, H.
Deposit date:2024-06-08
Release date:2025-06-11
Method:X-RAY DIFFRACTION (2.1 Å)
Cite:Development of pyrimidone derivatives as nonpeptidic and noncovalent 3-chymotrypsin-like protease (3CL pro ) inhibitors with anti-coronavirus activities.
Bioorg.Chem., 154, 2025
9FC2
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BU of 9fc2 by Molmil
The crystal structure of the SARS-CoV-2 receptor binding domain in complex with the neutralizing nanobody 4.
Descriptor: 1,2-ETHANEDIOL, 2-acetamido-2-deoxy-beta-D-glucopyranose, ACETATE ION, ...
Authors:Casasnovas, J.M, Fernandez, L.A, Silva, K.
Deposit date:2024-05-15
Release date:2025-06-11
Method:X-RAY DIFFRACTION (1.21 Å)
Cite:Integrating immune library probing with structure-based computational design to develop potent neutralizing nanobodies against emerging SARS-CoV-2 variants.
Mabs, 17, 2025
9GUB
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BU of 9gub by Molmil
SARS-CoV-2 Mac1 in complex with MCD-628
Descriptor: (2~{S})-3-(1~{H}-indol-3-yl)-2-(7~{H}-pyrrolo[2,3-d]pyrimidin-4-ylamino)propanoic acid, Papain-like protease nsp3
Authors:Duong, M, Paakkonen, J, Lehtio, L.
Deposit date:2024-09-19
Release date:2025-06-11
Last modified:2025-06-25
Method:X-RAY DIFFRACTION (1.1 Å)
Cite:Identification of a series of pyrrolo-pyrimidine-based SARS-CoV-2 Mac1 inhibitors that repress coronavirus replication.
Mbio, 16, 2025
9NPX
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BU of 9npx by Molmil
SARS-CoV-2 nsp1 bound to the Rhinolophus lepidus 40S ribosomal subunit (local refinement of the 40S body)
Descriptor: 18S ribosomal RNA, 40S ribosomal protein S11, 40S ribosomal protein S13, ...
Authors:Gen, R, Seattle Structural Genomics Center for Infectious Disease (SSGCID), Veesler, D.
Deposit date:2025-03-11
Release date:2025-06-11
Method:ELECTRON MICROSCOPY (2.1 Å)
Cite:SARS-CoV-2 nsp1 mediates broad inhibition of translation in mammals.
Cell Rep, 44, 2025
9C7X
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BU of 9c7x by Molmil
Crystal structure of SARS-CoV-2 antibody 1H06 in complex with a HR2 peptide
Descriptor: Heavy Chain of SARS-CoV-2 antibody 1H06, Light Chain of SARS-CoV-2 antibody 1H06, Spike protein S2'
Authors:Van Wazer, D.J, Zhou, T, Kwong, P.D.
Deposit date:2024-06-11
Release date:2025-06-18
Method:X-RAY DIFFRACTION (1.96 Å)
Cite:SARS-CoV-2 Peptide Immunization in Mice Elicits Broadly Neutralizing Antibodies Targeting Cryptic S2 Helical-Stem Epitope
To Be Published
9EEI
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BU of 9eei by Molmil
Crystal structure of the SARS-CoV-2 Omicron nsp5 main protease (Mpro) E166V mutant in complex with inhibitor 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:Neilsen, G, Kirby, K.A, Sarafianos, S.G.
Deposit date:2024-11-19
Release date:2025-06-18
Method:X-RAY DIFFRACTION (2.76 Å)
Cite:Strategy to overcome a nirmatrelvir resistance mechanism in the SARS-CoV-2 nsp5 protease.
Sci Adv, 11, 2025
9IKZ
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BU of 9ikz by Molmil
SARS-CoV-2 E-RTC bound to pRNA-nsp9 and GDP-BeF3-
Descriptor: BERYLLIUM TRIFLUORIDE ION, GUANOSINE-5'-DIPHOSPHATE, Helicase nsp13, ...
Authors:Yan, L.M, Huang, Y.C, Liu, Y.X, Rao, Z.H, Lou, Z.Y.
Deposit date:2024-06-29
Release date:2025-06-18
Method:ELECTRON MICROSCOPY (3.14 Å)
Cite:Substrate selection and transition reveal the mechanism for RNA capping catalyzed by SARS-CoV-2 NiRAN
To Be Published
9VAO
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BU of 9vao by Molmil
Crystal structure of Papain-like protease (PLpro) from SARS-CoV-2
Descriptor: GLYCEROL, PHOSPHATE ION, Papain-like protease nsp3, ...
Authors:Arya, R, Ganesh, J, Prashar, V, Kumar, M.
Deposit date:2025-06-03
Release date:2025-06-18
Method:X-RAY DIFFRACTION (1.82 Å)
Cite:Crystal structure of Papain-like protease (PLpro) from SARS-CoV-2
To Be Published
9CPP
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BU of 9cpp by Molmil
Crystal structure of SARS-CoV-2 receptor binding domain in complex with antibodies M22-17 and CC12.3
Descriptor: CC12.3 Fab heavy chain, CC12.3 Fab light chain, CITRIC ACID, ...
Authors:Feng, Z, Wilson, I.A.
Deposit date:2024-07-18
Release date:2025-06-25
Method:X-RAY DIFFRACTION (3.19 Å)
Cite:Structures of CR3022-like antibodies
To Be Published
9CPQ
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BU of 9cpq by Molmil
Crystal structure of SARS-CoV-2 receptor binding domain in complex with antibodies M22-44 and CC12.3
Descriptor: CC12.3 Fab heavy chain, CC12.3 Fab light chain, CITRIC ACID, ...
Authors:Feng, Z, Wilson, I.A.
Deposit date:2024-07-18
Release date:2025-06-25
Method:X-RAY DIFFRACTION (2.88 Å)
Cite:Structures of CR3022-like antibodies
To Be Published
9CPR
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BU of 9cpr by Molmil
Crystal structure of SARS-CoV-2 receptor binding domain in complex with antibodies M22-90 and CC12.3
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose, CC12.3 Fab heavy chain, CC12.3 Fab light chain, ...
Authors:Feng, Z, Wilson, I.A.
Deposit date:2024-07-18
Release date:2025-06-25
Method:X-RAY DIFFRACTION (3.1 Å)
Cite:Structures of CR3022-like antibodies
To Be Published
9CPS
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BU of 9cps by Molmil
Crystal structure of SARS-CoV-2 receptor binding domain in complex with antibodies M22-91 and CC12.3
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, CC12.3 Fab heavy chain, CC12.3 Fab light chain, ...
Authors:Feng, Z, Wilson, I.A.
Deposit date:2024-07-18
Release date:2025-06-25
Method:X-RAY DIFFRACTION (3.03 Å)
Cite:Structures of CR3022-like antibodies
To Be Published
9CPT
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BU of 9cpt by Molmil
Crystal structure of SARS-CoV-2 receptor binding domain in complex with antibodies M22-92 and CC12.3
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, CC12.3 Fab heavy chain, CC12.3 Fab light chain, ...
Authors:Feng, Z, Wilson, I.A.
Deposit date:2024-07-18
Release date:2025-06-25
Method:X-RAY DIFFRACTION (3.51 Å)
Cite:Structures of CR3022-like antibodies
To Be Published
9CPU
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BU of 9cpu by Molmil
Crystal structure of SARS-CoV-2 receptor binding domain in complex with antibodies C03-0304 and CC12.3
Descriptor: C03-0304 Fab heavy chain, C03-0304 Fab light chain, CC12.3 Fab heavy chain, ...
Authors:Feng, Z, Wilson, I.A.
Deposit date:2024-07-18
Release date:2025-06-25
Method:X-RAY DIFFRACTION (2.6 Å)
Cite:Structures of CR3022-like antibodies
To Be Published
9CPV
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BU of 9cpv by Molmil
Crystal structure of SARS-CoV-2 receptor binding domain in complex with antibodies C03-0614 and CC12.3
Descriptor: C03-0614 Fab heavy chain, C03-0614 Fab light chain, CC12.3 Fab heavy chain, ...
Authors:Feng, Z, Wilson, I.A.
Deposit date:2024-07-18
Release date:2025-06-25
Method:X-RAY DIFFRACTION (3 Å)
Cite:Structures of CR3022-like antibodies
To Be Published
9CPW
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BU of 9cpw by Molmil
Crystal structure of SARS-CoV-2 receptor binding domain in complex with antibodies C11-1036 and CC12.3
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, C11-1036 Fab heavy chain, C11-1036 Fab light chain, ...
Authors:Feng, Z, Wilson, I.A.
Deposit date:2024-07-18
Release date:2025-06-25
Method:X-RAY DIFFRACTION (3.1 Å)
Cite:Structures of CR3022-like antibodies
To Be Published
9CPX
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BU of 9cpx by Molmil
Crystal structure of SARS-CoV-2 receptor binding domain in complex with antibodies C03-0138 and CC12.3
Descriptor: C03-0138 Fab heavy chain, C03-0138 Fab light chain, CC12.3 Fab heavy chain, ...
Authors:Feng, Z, Wilson, I.A.
Deposit date:2024-07-18
Release date:2025-06-25
Method:X-RAY DIFFRACTION (2.7 Å)
Cite:Structures of CR3022-like antibodies
To Be Published

238582

數據於2025-07-09公開中

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