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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
7PS0
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BU of 7ps0 by Molmil
Crystal structure of the receptor binding domain of SARS-CoV-2 beta variant spike glycoprotein in complex with beta-24 Fabs
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, Beta-24 heavy chain, Beta-24 light chain, ...
Authors:Zhou, D, Ren, J, Stuart, D.I.
Deposit date:2021-09-22
Release date:2021-12-15
Last modified:2024-01-31
Method:X-RAY DIFFRACTION (2.92 Å)
Cite:The antibody response to SARS-CoV-2 Beta underscores the antigenic distance to other variants.
Cell Host Microbe, 30, 2022
7PS1
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BU of 7ps1 by Molmil
Crystal structure of the receptor binding domain of SARS-CoV-2 beta variant spike glycoprotein in complex with Beta-27 Fab
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, Beta-27 Fab heavy chain, Beta-27 Fab light chain, ...
Authors:Zhou, D, Ren, J, Stuart, D.I.
Deposit date:2021-09-22
Release date:2021-12-15
Last modified:2024-01-31
Method:X-RAY DIFFRACTION (2.4 Å)
Cite:The antibody response to SARS-CoV-2 Beta underscores the antigenic distance to other variants.
Cell Host Microbe, 30, 2022
7PS2
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BU of 7ps2 by Molmil
Crystal structure of the receptor binding domain of SARS-CoV-2 beta variant spike glycoprotein in complex with Beta-29 and Beta-53 Fabs
Descriptor: Beta-29 Fab heavy chain, Beta-29 Fab light chain, Beta-53 Fab light chain, ...
Authors:Zhou, D, Ren, J, Stuart, D.I.
Deposit date:2021-09-22
Release date:2021-12-15
Last modified:2024-01-31
Method:X-RAY DIFFRACTION (2.99 Å)
Cite:The antibody response to SARS-CoV-2 Beta underscores the antigenic distance to other variants.
Cell Host Microbe, 30, 2022
7PS4
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BU of 7ps4 by Molmil
Crystal structure of the receptor binding domain of SARS-CoV-2 beta variant spike glycoprotein in complex with Beta-38
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Beta-38 Fab heavy chain, Beta-38 Fab light chain, ...
Authors:Zhou, D, Ren, J, Stuart, D.I.
Deposit date:2021-09-22
Release date:2021-12-15
Last modified:2024-01-31
Method:X-RAY DIFFRACTION (1.94 Å)
Cite:The antibody response to SARS-CoV-2 Beta underscores the antigenic distance to other variants.
Cell Host Microbe, 30, 2022
7PS5
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BU of 7ps5 by Molmil
Crystal structure of the receptor binding domain of SARS-CoV-2 beta variant spike glycoprotein in complex with Beta-47 Fab
Descriptor: Beta-47 Fab heavy chain, Beta-47 Fab light chain, Spike protein S1, ...
Authors:Zhou, D, Ren, J, Stuart, D.I.
Deposit date:2021-09-22
Release date:2021-12-15
Last modified:2024-01-31
Method:X-RAY DIFFRACTION (3.14 Å)
Cite:The antibody response to SARS-CoV-2 Beta underscores the antigenic distance to other variants.
Cell Host Microbe, 30, 2022
7PS6
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BU of 7ps6 by Molmil
Crystal structure of the receptor binding domain of SARS-CoV-2 beta variant spike glycoprotein in complex with Beta-44 and Beta-54 Fabs
Descriptor: 2-(2-METHOXYETHOXY)ETHANOL, Beta-44 Fab heavy chain, Beta-44 Fab light chain, ...
Authors:Zhou, D, Ren, J, Stuart, D.I.
Deposit date:2021-09-22
Release date:2021-12-15
Last modified:2024-01-31
Method:X-RAY DIFFRACTION (2.26 Å)
Cite:The antibody response to SARS-CoV-2 Beta underscores the antigenic distance to other variants.
Cell Host Microbe, 30, 2022
7PS7
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BU of 7ps7 by Molmil
Crystal structure of the receptor binding domain of SARS-CoV-2 beta variant spike glycoprotein in complex with Beta-40 Fab
Descriptor: Beta-40 Fab light chain, Beta-40 heavy chain, Spike protein S1
Authors:Zhou, D, Ren, J, Stuart, D.I.
Deposit date:2021-09-22
Release date:2021-12-15
Last modified:2024-01-31
Method:X-RAY DIFFRACTION (3.9 Å)
Cite:The antibody response to SARS-CoV-2 Beta underscores the antigenic distance to other variants.
Cell Host Microbe, 30, 2022
7Q6E
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BU of 7q6e by Molmil
Beta049 fab in complex with SARS-CoV2 beta-Spike glycoprotein, The Beta mAb response underscores the antigenic distance to other SARS-CoV-2 variants
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Beta-49 heavy chain, ...
Authors:Duyvesteyn, H.M.E, Ren, J, Stuart, D.I.
Deposit date:2021-11-07
Release date:2021-12-15
Last modified:2022-01-26
Method:ELECTRON MICROSCOPY (2.7 Å)
Cite:The antibody response to SARS-CoV-2 Beta underscores the antigenic distance to other variants.
Cell Host Microbe, 30, 2022
7Q9F
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BU of 7q9f by Molmil
Beta-50 fab in complex with SARS-CoV-2 beta-Spike glycoprotein
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:Duyvesteyn, H.M.E, Ren, J, Stuart, D.I.
Deposit date:2021-11-12
Release date:2021-12-15
Last modified:2022-01-26
Method:ELECTRON MICROSCOPY (3.6 Å)
Cite:The antibody response to SARS-CoV-2 Beta underscores the antigenic distance to other variants.
Cell Host Microbe, 30, 2022
7Q9G
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BU of 7q9g by Molmil
COVOX-222 fab in complex with SARS-CoV-2 beta-Spike glycoprotein
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, COVOX-222 heavy chain, ...
Authors:Duyvesteyn, H.M.E, Ren, J, Stuart, D.I.
Deposit date:2021-11-12
Release date:2021-12-15
Last modified:2022-01-26
Method:ELECTRON MICROSCOPY (3.3 Å)
Cite:The antibody response to SARS-CoV-2 Beta underscores the antigenic distance to other variants.
Cell Host Microbe, 30, 2022
7Q9I
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BU of 7q9i by Molmil
Beta-43 fab in complex with SARS-CoV-2 beta-Spike glycoprotein
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Beta-43 heavy chain, ...
Authors:Duyvesteyn, H.M.E, Ren, J, Stuart, D.I.
Deposit date:2021-11-12
Release date:2021-12-15
Last modified:2022-01-26
Method:ELECTRON MICROSCOPY (4.9 Å)
Cite:The antibody response to SARS-CoV-2 Beta underscores the antigenic distance to other variants.
Cell Host Microbe, 30, 2022
7Q9J
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BU of 7q9j by Molmil
Beta-26 fab in complex with SARS-CoV-2 beta-Spike glycoprotein
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Beta-26 heavy chain, ...
Authors:Duyvesteyn, H.M.E, Ren, J, Stuart, D.I.
Deposit date:2021-11-12
Release date:2021-12-15
Last modified:2022-01-26
Method:ELECTRON MICROSCOPY (4 Å)
Cite:The antibody response to SARS-CoV-2 Beta underscores the antigenic distance to other variants.
Cell Host Microbe, 30, 2022
7Q9K
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BU of 7q9k by Molmil
Beta-32 fab in complex with SARS-CoV-2 beta-Spike glycoprotein
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Beta-32 heavy chain, ...
Authors:Duyvesteyn, H.M.E, Ren, J, Stuart, D.I.
Deposit date:2021-11-12
Release date:2021-12-15
Last modified:2022-01-26
Method:ELECTRON MICROSCOPY (4.5 Å)
Cite:The antibody response to SARS-CoV-2 Beta underscores the antigenic distance to other variants.
Cell Host Microbe, 30, 2022
7Q9M
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BU of 7q9m by Molmil
Beta-53 fab in complex with SARS-CoV-2 beta-Spike glycoprotein
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Beta-53 fab heavy chain, ...
Authors:Duyvesteyn, H.M.E, Ren, J, Stuart, D.I.
Deposit date:2021-11-12
Release date:2021-12-15
Last modified:2022-01-26
Method:ELECTRON MICROSCOPY (3.7 Å)
Cite:The antibody response to SARS-CoV-2 Beta underscores the antigenic distance to other variants.
Cell Host Microbe, 30, 2022
7Q9P
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BU of 7q9p by Molmil
Beta-06 fab in complex with SARS-CoV-2 beta-Spike glycoprotein
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Beta-06 heavy chain, ...
Authors:Duyvesteyn, H.M.E, Ren, J, Stuart, D.I.
Deposit date:2021-11-12
Release date:2021-12-15
Last modified:2022-01-26
Method:ELECTRON MICROSCOPY (4.5 Å)
Cite:The antibody response to SARS-CoV-2 Beta underscores the antigenic distance to other variants.
Cell Host Microbe, 30, 2022
7QG7
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BU of 7qg7 by Molmil
SARS-CoV-2 macrodomain Nsp3b bound to the remdesivir nucleoside GS-441524
Descriptor: (2~{R},3~{R},4~{S},5~{R})-2-(4-azanylpyrrolo[2,1-f][1,2,4]triazin-7-yl)-5-(hydroxymethyl)-3,4-bis(oxidanyl)oxolane-2-carbonitrile, 1,2-ETHANEDIOL, Papain-like protease nsp3
Authors:Wollenhaupt, J, Linhard, V, Sreeramulu, S, Weiss, M.S, Schwalbe, H.
Deposit date:2021-12-07
Release date:2021-12-15
Last modified:2024-01-31
Method:X-RAY DIFFRACTION (1.72 Å)
Cite:Binding Adaptation of GS-441524 Diversifies Macro Domains and Downregulates SARS-CoV-2 de-MARylation Capacity.
J.Mol.Biol., 434, 2022
7RPV
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BU of 7rpv by Molmil
Crystal structure of affinity-enhancing and catalytically inactive ACE2 in complex with SARS-CoV-2 RBD
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, Processed angiotensin-converting enzyme 2, Spike protein S1, ...
Authors:Chen, Y, Tolbert, D.W, Pazgier, M.
Deposit date:2021-08-04
Release date:2021-12-15
Last modified:2023-10-18
Method:X-RAY DIFFRACTION (3.54 Å)
Cite:Engineered ACE2-Fc counters murine lethal SARS-CoV-2 infection through direct neutralization and Fc-effector activities.
Biorxiv, 2021
7FAE
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BU of 7fae by Molmil
S protein of SARS-CoV-2 in complex bound with P36-5D2(state2)
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, P36-5D2 heavy chain, ...
Authors:Zhang, L, Wang, X, Shan, S, Zhang, S.
Deposit date:2021-07-06
Release date:2021-12-22
Last modified:2022-02-16
Method:ELECTRON MICROSCOPY (3.65 Å)
Cite:A Potent and Protective Human Neutralizing Antibody Against SARS-CoV-2 Variants.
Front Immunol, 12, 2021
7FAF
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BU of 7faf by Molmil
S protein of SARS-CoV-2 in complex bound with P36-5D2 (state1)
Descriptor: P36-5D2 heavy chain, P36-5D2 light chain, Spike glycoprotein
Authors:Zhang, L, Wang, X, Zhang, S, Shan, S.
Deposit date:2021-07-06
Release date:2021-12-22
Last modified:2022-02-16
Method:ELECTRON MICROSCOPY (3.69 Å)
Cite:A Potent and Protective Human Neutralizing Antibody Against SARS-CoV-2 Variants.
Front Immunol, 12, 2021
7MLF
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BU of 7mlf by Molmil
Crystal Structure of SARS-CoV-2 Main Protease (3CLpro/Mpro) Covalently Bound to Compound C7
Descriptor: 3C-like proteinase, N-(4-tert-butylphenyl)-2-chloro-N-[(1R)-2-(cyclohexylamino)-2-oxo-1-(pyridin-3-yl)ethyl]acetamide
Authors:Sharon, I, Stille, J, Tjutrins, J, Wang, G, Venegas, F.A, Hennecker, C, Rueda, A.M, Miron, C.E, Pinus, S, Labarre, A, Patrascu, M.B, Vlaho, D, Huot, M, Mittermaier, A.K, Moitessier, N, Schmeing, T.M.
Deposit date:2021-04-28
Release date:2021-12-22
Last modified:2023-10-18
Method:X-RAY DIFFRACTION (2.6 Å)
Cite:Design, synthesis and in vitro evaluation of novel SARS-CoV-2 3CL pro covalent inhibitors.
Eur.J.Med.Chem., 229, 2021
7MLG
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BU of 7mlg by Molmil
Crystal Structure of SARS-CoV-2 Main Protease (3CLpro/Mpro) Covalently Bound to Compound C63
Descriptor: (2R)-2-[(4-tert-butylphenyl)(ethanesulfonyl)amino]-N-cyclohexyl-2-(pyridin-3-yl)acetamide, 3C-like proteinase
Authors:Sharon, I, Stille, J, Tjutrins, J, Wang, G, Venegas, F.A, Hennecker, C, Rueda, A.M, Miron, C.E, Pinus, S, Labarre, A, Patrascu, M.B, Vlaho, D, Huot, M, Mittermaier, A.K, Moitessier, N, Schmeing, T.M.
Deposit date:2021-04-28
Release date:2021-12-22
Last modified:2023-10-18
Method:X-RAY DIFFRACTION (2.5 Å)
Cite:Design, synthesis and in vitro evaluation of novel SARS-CoV-2 3CL pro covalent inhibitors.
Eur.J.Med.Chem., 229, 2021
7Q0G
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BU of 7q0g by Molmil
Crystal structure of the receptor binding domain of SARS-CoV-2 beta variant spike glycoprotein in complex with Beta-49 and FI-3A Fabs
Descriptor: Beta-49 Fab heavy chain, Beta-49 Fab light chain, CHLORIDE ION, ...
Authors:Zhou, D, Ren, J, Stuart, D.I.
Deposit date:2021-10-14
Release date:2021-12-22
Last modified:2024-01-31
Method:X-RAY DIFFRACTION (1.82 Å)
Cite:The antibody response to SARS-CoV-2 Beta underscores the antigenic distance to other variants.
Cell Host Microbe, 30, 2022
7Q0H
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BU of 7q0h by Molmil
Crystal structure of the receptor binding domain of SARS-CoV-2 beta variant spike glycoprotein in complex with Beta-50 and Beta-54
Descriptor: Beta-50 Fab heavy chain, Beta-50 Fab light chain, Beta-54 Fab heavy chain, ...
Authors:Zhou, D, Ren, J, Stuart, D.I.
Deposit date:2021-10-14
Release date:2021-12-22
Last modified:2024-01-31
Method:X-RAY DIFFRACTION (3.65 Å)
Cite:The antibody response to SARS-CoV-2 Beta underscores the antigenic distance to other variants.
Cell Host Microbe, 30, 2022
7Q0I
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BU of 7q0i by Molmil
Crystal structure of the N-terminal domain of SARS-CoV-2 beta variant spike glycoprotein in complex with Beta-43
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:Zhou, D, Ren, J, Stuart, D.I.
Deposit date:2021-10-14
Release date:2021-12-22
Last modified:2024-01-31
Method:X-RAY DIFFRACTION (2.39 Å)
Cite:The antibody response to SARS-CoV-2 Beta underscores the antigenic distance to other variants.
Cell Host Microbe, 30, 2022
7T42
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BU of 7t42 by Molmil
Structure of SARS-CoV-2 3CL protease in complex with inhibitor 2c
Descriptor: (1R,2S)-1-hydroxy-2-{[N-({[2-(2-methylpropanoyl)-2-azaspiro[3.3]heptan-6-yl]oxy}carbonyl)-L-leucyl]amino}-3-[(3S)-2-oxopyrrolidin-3-yl]propane-1-sulfonic acid, (1S,2S)-2-[(N-{[(2-acetyl-2-azaspiro[3.3]heptan-6-yl)oxy]carbonyl}-L-leucyl)amino]-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propane-1-sulfonic acid, 3C-like proteinase, ...
Authors:Liu, L, Lovell, S, Battaile, K.P, Chamandi, S.D, Kim, Y, Groutas, W.C, Chang, K.O.
Deposit date:2021-12-09
Release date:2021-12-22
Last modified:2023-10-18
Method:X-RAY DIFFRACTION (1.6 Å)
Cite:Structure-Guided Design of Potent Spirocyclic Inhibitors of Severe Acute Respiratory Syndrome Coronavirus-2 3C-like Protease.
J.Med.Chem., 65, 2022

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數據於2024-07-10公開中

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