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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
8R6E
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BU of 8r6e by Molmil
SARS-CoV-2 Nucleocapsid dimerization domain
Descriptor: 1,2-ETHANEDIOL, DI(HYDROXYETHYL)ETHER, GLYCEROL, ...
Authors:Fahoum, J, Wiener, R, Rouvinski, A, Isupov, M.N.
Deposit date:2023-11-22
Release date:2024-12-04
Method:X-RAY DIFFRACTION (1.53 Å)
Cite:SARS-CoV-2 Nucleocapsid dimerization domain
To Be Published
8RNE
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HLA-E*01:03 in complex with SARS-CoV-2 Nsp13 peptide, VMPLSAPTL
Descriptor: Beta-2-microglobulin, HLA class I histocompatibility antigen, E alpha chain variant, ...
Authors:Sun, R, Achour, A, Sala, B.M, Sandalova, T.
Deposit date:2024-01-09
Release date:2024-12-04
Last modified:2025-01-22
Method:X-RAY DIFFRACTION (1.71 Å)
Cite:Emerging mutation in SARS-CoV-2 facilitates escape from NK cell recognition and associates with enhanced viral fitness.
Plos Pathog., 20, 2024
8RNF
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HLA-E*01:03 in complex with SARS-CoV-2 Omicron Nsp13 peptide, VIPLSAPTL
Descriptor: Beta-2-microglobulin, HLA class I histocompatibility antigen, E alpha chain variant, ...
Authors:Sun, R, Achour, A, Sala, B.M, Sandalova, T.
Deposit date:2024-01-09
Release date:2024-12-04
Last modified:2025-01-22
Method:X-RAY DIFFRACTION (1.872 Å)
Cite:Emerging mutation in SARS-CoV-2 facilitates escape from NK cell recognition and associates with enhanced viral fitness.
Plos Pathog., 20, 2024
8USZ
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Cryo-EM Structure of Full-Length Spike Protein of Omicron XBB.1.5
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:Huynh, K.W, Chang, J.S, Fennell, K.F, Che, Y, Wu, H.
Deposit date:2023-10-30
Release date:2024-12-04
Last modified:2025-05-21
Method:ELECTRON MICROSCOPY (2.98 Å)
Cite:Preclinical characterization of the Omicron XBB.1.5-adapted BNT162b2 COVID-19 vaccine.
Npj Vaccines, 9, 2024
8XKO
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CryoEM structure of compound HNC-1664 bound with RdRP-RNA complex of SARS-CoV-2
Descriptor: MAGNESIUM ION, Non-structural protein 7, Non-structural protein 8, ...
Authors:Li, M, An, L, Hong, Y, Li, S, Zhang, K.
Deposit date:2023-12-23
Release date:2024-12-04
Last modified:2025-07-02
Method:ELECTRON MICROSCOPY (3.29 Å)
Cite:An adenosine analog shows high antiviral potency against coronavirus and arenavirus mainly through an unusual base pairing mode.
Nat Commun, 15, 2024
8YX2
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BU of 8yx2 by Molmil
Crystal Structure of SARS CoV-2 Papain-like Protease PLpro-C111S in Complex with GZNL-P4
Descriptor: Papain-like protease nsp3, ZINC ION, ~{N}-[1-(1,2-dihydroacenaphthylen-5-yl)cyclopropyl]-2-methyl-5-(4-methylpiperazin-1-yl)benzamide
Authors:Lu, Y, Shang, J.
Deposit date:2024-04-02
Release date:2024-12-04
Method:X-RAY DIFFRACTION (2.31 Å)
Cite:Discovery of orally bioavailable SARS-CoV-2 papain-like protease inhibitor as a potential treatment for COVID-19.
Nat Commun, 15, 2024
8YX3
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BU of 8yx3 by Molmil
Crystal Structure of SARS CoV-2 Papain-like Protease PLpro-C111S in Complex with GZNL-P28
Descriptor: Papain-like protease nsp3, ~{N}-[1-(1,2-dihydroacenaphthylen-5-yl)cyclopropyl]-5-[(3~{S})-4-ethyl-3-methyl-piperazin-1-yl]-2-methyl-benzamide
Authors:Lu, Y, Shang, J.
Deposit date:2024-04-02
Release date:2024-12-04
Method:X-RAY DIFFRACTION (2.6 Å)
Cite:Discovery of orally bioavailable SARS-CoV-2 papain-like protease inhibitor as a potential treatment for COVID-19.
Nat Commun, 15, 2024
8YX4
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Crystal Structure of SARS CoV-2 Papain-like Protease PLpro-C111S in Complex with GZNL-P31
Descriptor: 2-methyl-~{N}-[1-(1-methyl-2-oxidanylidene-benzo[cd]indol-6-yl)cyclopropyl]-5-[3-(4-methyl-4-oxidanyl-piperidin-1-yl)azetidin-1-yl]benzamide, CADMIUM ION, CHLORIDE ION, ...
Authors:Lu, Y, Shang, J.
Deposit date:2024-04-02
Release date:2024-12-04
Method:X-RAY DIFFRACTION (2.28 Å)
Cite:Discovery of orally bioavailable SARS-CoV-2 papain-like protease inhibitor as a potential treatment for COVID-19.
Nat Commun, 15, 2024
8YX5
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Crystal Structure of SARS CoV-2 Papain-like Protease PLpro-C111S in Complex with GZNL-P35
Descriptor: 5-[(1~{R},5~{S})-3,6-diazabicyclo[3.1.1]heptan-3-yl]-2-methyl-~{N}-[1-(1-methyl-2-oxidanylidene-benzo[cd]indol-6-yl)cyclopropyl]benzamide, GLYCEROL, Papain-like protease nsp3, ...
Authors:Lu, Y, Shang, J.
Deposit date:2024-04-02
Release date:2024-12-04
Method:X-RAY DIFFRACTION (1.74 Å)
Cite:Discovery of orally bioavailable SARS-CoV-2 papain-like protease inhibitor as a potential treatment for COVID-19.
Nat Commun, 15, 2024
9B82
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BU of 9b82 by Molmil
Crystal structure of SARS-CoV-2 receptor binding domain in complex with neutralizing antibody COVA2-15
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, COVA2-15 antibody heavy chain, COVA2-15 antibody light chain, ...
Authors:Yuan, M, Zhu, X, Wilson, I.A.
Deposit date:2024-03-28
Release date:2024-12-04
Last modified:2025-01-08
Method:X-RAY DIFFRACTION (3.38 Å)
Cite:Plant-produced SARS-CoV-2 antibody engineered towards enhanced potency and in vivo efficacy.
Plant Biotechnol J, 23, 2025
9GLV
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BU of 9glv by Molmil
Crystal structure of SARS-CoV-2 Mpro with AB-343.
Descriptor: (1S,3S,4S)-N-[(2S)-1-azanylidene-3-[(3S)-5,5-dimethyl-2-oxidanylidene-pyrrolidin-3-yl]propan-2-yl]-2-[(2R)-3-cyclobutyl-2-[2,2,2-tris(fluoranyl)ethanoylamino]propanoyl]-5,5-bis(fluoranyl)-2-azabicyclo[2.2.2]octane-3-carboxamide, 1,2-ETHANEDIOL, 3C-like proteinase nsp5, ...
Authors:Prasad, A, Blaesse, M, Maskos, K, Steinbacher, S, Konz Makino, D.L.
Deposit date:2024-08-28
Release date:2024-12-04
Last modified:2024-12-11
Method:X-RAY DIFFRACTION (1.93 Å)
Cite:Biological characterization of AB-343, a novel and potent SARS-CoV-2 M pro inhibitor with pan-coronavirus activity.
Antiviral Res., 232, 2024
9GUD
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BU of 9gud by Molmil
SARS-CoV-2 methyltransferase nsp10-16 in complex with SAM and theophylline derivative LAS 54570922
Descriptor: (3~{S})-3-azanyl-4-[(3~{R},4~{R},6~{S})-3-[1,3-dimethyl-2,6-bis(oxidanylidene)purin-7-yl]-4-methyl-4,6-bis(oxidanyl)azepan-1-yl]-4-oxidanylidene-butanoic acid, 1,2-ETHANEDIOL, 2'-O-methyltransferase nsp16, ...
Authors:Kremling, V, Sprenger, J, Oberthuer, D, Kiene, A.
Deposit date:2024-09-19
Release date:2024-12-04
Method:X-RAY DIFFRACTION (2.05 Å)
Cite:Crystal structures of SARS-CoV-2 methyltransferase nsp10-16 with Cap0-site binders
To Be Published
9GUY
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BU of 9guy by Molmil
SARS-CoV-2 methyltransferase nsp10-16 in complex with SAM and theophylline derivative LAS 54571098
Descriptor: 1,2-ETHANEDIOL, 2'-O-methyltransferase nsp16, 2-(N-MORPHOLINO)-ETHANESULFONIC ACID, ...
Authors:Kremling, V, Sprenger, J, Oberthuer, D, Kiene, A.
Deposit date:2024-09-20
Release date:2024-12-04
Method:X-RAY DIFFRACTION (2.1 Å)
Cite:Crystal structures of SARS-CoV-2 methyltransferase nsp10-16 with Cap0-site binders
To Be Published
9HAK
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BU of 9hak by Molmil
Structure of compound 119 bound to SARS-CoV-2 main protease
Descriptor: (5~{R})-4-[(4-bromanyl-2-ethyl-phenyl)methyl]-~{N}-ethyl-1-thieno[2,3-c]pyridin-4-ylcarbonyl-1,4-diazepane-5-carboxamide, 3C-like proteinase nsp5, CHLORIDE ION, ...
Authors:Mac Sweeney, A, Hazemann, J.
Deposit date:2024-11-04
Release date:2024-12-04
Last modified:2025-05-07
Method:X-RAY DIFFRACTION (1.25 Å)
Cite:Accelerating the Hit-To-Lead Optimization of a SARS-CoV-2 Mpro Inhibitor Series by Combining High-Throughput Medicinal Chemistry and Computational Simulations.
J.Med.Chem., 68, 2025
8RBY
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BU of 8rby by Molmil
The crystal structure of the SARS-CoV-2 receptor binding domain in complex with the neutralizing nanobody 1.26
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, 3[N-MORPHOLINO]PROPANE SULFONIC ACID, Camel-derived nanobody 1.26, ...
Authors:Casasnovas, J.M, Fernandez, L.A, Silva, K.
Deposit date:2023-12-05
Release date:2024-12-11
Method:X-RAY DIFFRACTION (1.9 Å)
Cite:The crystal structure of the SARS-CoV-2 receptor binding domain in complex with the neutralizing nanobody 1.26
To Be Published
8XEF
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BU of 8xef by Molmil
Cocktail GC2050-GC2225
Descriptor: GC2050 heavy chain, GC2050 light chain, GC2225 heavy chain, ...
Authors:Feng, L.L.
Deposit date:2023-12-11
Release date:2024-12-11
Last modified:2025-07-02
Method:ELECTRON MICROSCOPY (4.41 Å)
Cite:XBB.1.5 RBD in complex with GC2050 and GC2225
To Be Published
9CJ6
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BU of 9cj6 by Molmil
Crystal Structure of SARS-CoV-2 N-NTD with part of N-arm complex with ssDNA.
Descriptor: DNA (5'-D(P*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*T)-3'), Nucleoprotein
Authors:Maiti, A, Matsuo, H.
Deposit date:2024-07-05
Release date:2024-12-11
Last modified:2025-01-22
Method:X-RAY DIFFRACTION (1.55 Å)
Cite:Affinity Tag-Free Purification of SARS-CoV-2 N Protein and Its Crystal Structure in Complex with ssDNA.
Biomolecules, 14, 2024
9HJH
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BU of 9hjh by Molmil
Structure of compound 1 bound to SARS-CoV-2 main protease
Descriptor: (2~{R})-4-[(4-bromanyl-2-ethyl-phenyl)methyl]-1-(5-chloranylpyridin-3-yl)carbonyl-~{N}-ethyl-1,4-diazepane-2-carboxamide, 1,2-ETHANEDIOL, 3C-like proteinase nsp5, ...
Authors:Mac Sweeney, A, Hazemann, J.
Deposit date:2024-11-29
Release date:2024-12-11
Last modified:2025-05-07
Method:X-RAY DIFFRACTION (1.2 Å)
Cite:Accelerating the Hit-To-Lead Optimization of a SARS-CoV-2 Mpro Inhibitor Series by Combining High-Throughput Medicinal Chemistry and Computational Simulations.
J.Med.Chem., 68, 2025
8JAP
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BU of 8jap by Molmil
Cryo-EM structure of SARS-CoV-2 WT RBD in complex with W328-6H2 (local refinement)
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, H chain of W328-6H2 Fab region, L chain of W328-6H2 Fab region, ...
Authors:Nan, X.Y, Li, Y.J.
Deposit date:2023-05-06
Release date:2024-12-18
Method:ELECTRON MICROSCOPY (3.81 Å)
Cite:Cryo-EM structure of SARS-CoV-2 WT RBD in complex with W328-6H2 (local refinement)
To Be Published
8TYK
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BU of 8tyk by Molmil
Crystal Structure of SARS-CoV-2 Main Protease (Mpro) T21I Mutant
Descriptor: 3C-like proteinase
Authors:Kohaal, N, Lewandowski, E.M, Wang, J, Chen, Y.
Deposit date:2023-08-25
Release date:2024-12-18
Method:X-RAY DIFFRACTION (1.98 Å)
Cite:Crystal Structure of SARS-CoV-2 Main Protease (Mpro) T21I Mutant
To Be Published
8V5V
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BU of 8v5v by Molmil
Structure of a SARS-CoV-2 spike S2 subunit in a pre-fusion, open 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 protein S2,Fibritin, ...
Authors:Olmedillas, E, Diaz, R, Hastie, K, Ollmann-Saphire, E.
Deposit date:2023-12-01
Release date:2024-12-18
Method:ELECTRON MICROSCOPY (2.93 Å)
Cite:Structure of a SARS-CoV-2 spike S2 subunit in a pre-fusion, open conformation
To Be Published
8XRQ
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BU of 8xrq by Molmil
SARS-CoV-2 BA.1 spike RBD in complex bound with VacBB-639
Descriptor: Heavy chain of VacBB 639 Fab, Light chain of VacBB 639 Fab, Spike protein S1
Authors:Liu, C.C, Ju, B, Zhang, Z.
Deposit date:2024-01-08
Release date:2024-12-18
Last modified:2025-03-26
Method:ELECTRON MICROSCOPY (4.19 Å)
Cite:Rapid clonal expansion and somatic hypermutation contribute to the fate of SARS-CoV-2 broadly neutralizing antibodies.
J Immunol., 214, 2025
9BIH
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BU of 9bih by Molmil
SARS-CoV-2 endoribonuclease Nsp15 bound to dsRNA with 1 nucleotide bulge
Descriptor: RNA (34-mer), RNA (35-mer), Uridylate-specific endoribonuclease nsp15
Authors:Wright, Z.M, Butay, K.J, Krahn, J.M, Borgnia, M.J, Stanley, R.E.
Deposit date:2024-04-23
Release date:2024-12-18
Last modified:2025-01-15
Method:ELECTRON MICROSCOPY (3.24 Å)
Cite:Spontaneous base flipping helps drive Nsp15's preferences in double stranded RNA substrates.
Nat Commun, 16, 2025
8UDF
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BU of 8udf by Molmil
Crystal structure of SARS-CoV-2 3CL protease with inhibitor DEL_7
Descriptor: 2-cyano-D-phenylalanyl-2,4-dichloro-N-[(2S)-1-(4-fluorophenyl)-4-(methylamino)-4-oxobutan-2-yl]-D-phenylalaninamide, 3C-like proteinase nsp5, CHLORIDE ION, ...
Authors:Forouhar, F, Liu, H, Zack, A, Iketani, S, Williams, A, Vaz, D.R, Habashi, D.L, Resnick, S.J, Chavez, A, Ho, D.D, Stockwell, B.R.
Deposit date:2023-09-28
Release date:2024-12-25
Last modified:2025-01-15
Method:X-RAY DIFFRACTION (1.74 Å)
Cite:Development of small molecule non-covalent coronavirus 3CL protease inhibitors from DNA-encoded chemical library screening.
Nat Commun, 16, 2025
8UDJ
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BU of 8udj by Molmil
Crystal structure of SARS-CoV-2 3CL protease with inhibitor DEL_2
Descriptor: 2-cyano-D-phenylalanyl-2,4-dichloro-N-[(2S)-4-(methylamino)-4-oxo-1-phenylbutan-2-yl]-D-phenylalaninamide, 3C-like proteinase nsp5
Authors:Forouhar, F, Liu, H, Zack, A, Iketani, S, Williams, A, Vaz, D.R, Habashi, D.L, Resnick, S.J, Chavez, A, Ho, D.D, Stockwell, B.R.
Deposit date:2023-09-28
Release date:2024-12-25
Last modified:2025-01-15
Method:X-RAY DIFFRACTION (1.85 Å)
Cite:Development of small molecule non-covalent coronavirus 3CL protease inhibitors from DNA-encoded chemical library screening.
Nat Commun, 16, 2025

238582

數據於2025-07-09公開中

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