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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
7F5R
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Crystal structure of SARS-CoV-2 Y453F-RBD bound to mink ACE2
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 S1, ...
Authors:Wang, X.Q, Ding, Q, Lan, J, Ren, W.L.
Deposit date:2021-06-22
Release date:2022-06-22
Last modified:2023-11-29
Method:X-RAY DIFFRACTION (3.01 Å)
Cite:Crystal structure of SARS-CoV-2 Y453F-RBD bound to mink ACE2
To Be Published
7FC5
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BU of 7fc5 by Molmil
Crystal structure of SARS-CoV-2 RBD and horse ACE2
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, Angiotensin-converting enzyme, Spike protein S1
Authors:Wang, X.Q, Lan, J, Ge, J.W.
Deposit date:2021-07-13
Release date:2022-06-22
Last modified:2023-11-29
Method:X-RAY DIFFRACTION (2.894 Å)
Cite:Structural insights into the binding of SARS-CoV-2, SARS-CoV, and hCoV-NL63 spike receptor-binding domain to horse ACE2.
Structure, 30, 2022
7MB4
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BU of 7mb4 by Molmil
SARS-CoV-2 Main Protease (Mpro) C145A in Complex with Cleavage Site Nsp4/5 (P6-P1)
Descriptor: 3C-like proteinase, THR-SER-ALA-VAL-LEU-GLN
Authors:Lockbaum, G.J, Schiffer, C.A.
Deposit date:2021-03-31
Release date:2022-06-22
Last modified:2023-10-18
Method:X-RAY DIFFRACTION (1.83 Å)
Cite:Defining the substrate envelope of SARS-CoV-2 main protease to predict and avoid drug resistance.
Nat Commun, 13, 2022
7MB5
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BU of 7mb5 by Molmil
SARS-CoV-2 Main Protease (Mpro) C145A in Complex with Cleavage Site Nsp5/6 (P6-P1)
Descriptor: 3C-like proteinase, SER-GLY-VAL-THR-PHE-GLN
Authors:Lockbaum, G.J, Schiffer, C.A.
Deposit date:2021-03-31
Release date:2022-06-22
Last modified:2023-10-18
Method:X-RAY DIFFRACTION (1.6 Å)
Cite:Defining the substrate envelope of SARS-CoV-2 main protease to predict and avoid drug resistance.
Nat Commun, 13, 2022
7MB6
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BU of 7mb6 by Molmil
SARS-CoV-2 Main Protease (Mpro) C145A in Complex with Cleavage Site Nsp6/7 (P6-P1)
Descriptor: 3C-like proteinase, LYS-VAL-ALA-THR-VAL-GLN
Authors:Lockbaum, G.J, Schiffer, C.A.
Deposit date:2021-03-31
Release date:2022-06-22
Last modified:2023-10-18
Method:X-RAY DIFFRACTION (2.21 Å)
Cite:Defining the substrate envelope of SARS-CoV-2 main protease to predict and avoid drug resistance.
Nat Commun, 13, 2022
7MB7
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BU of 7mb7 by Molmil
SARS-CoV-2 Main Protease (Mpro) C145A in Complex with Cleavage Site Nsp7/8 (P6-P1)
Descriptor: 3C-like proteinase, ASN-ARG-ALA-THR-LEU-GLN
Authors:Lockbaum, G.J, Schiffer, C.A.
Deposit date:2021-03-31
Release date:2022-06-22
Last modified:2023-10-18
Method:X-RAY DIFFRACTION (2.02 Å)
Cite:Defining the substrate envelope of SARS-CoV-2 main protease to predict and avoid drug resistance.
Nat Commun, 13, 2022
7MB8
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BU of 7mb8 by Molmil
SARS-CoV-2 Main Protease (Mpro) C145A in Complex with Cleavage Site Nsp8/9 (P6-P1)
Descriptor: 3C-like proteinase, SER-ALA-VAL-LYS-LEU-GLN
Authors:Lockbaum, G.J, Schiffer, C.A.
Deposit date:2021-03-31
Release date:2022-06-22
Last modified:2023-10-18
Method:X-RAY DIFFRACTION (1.62 Å)
Cite:Defining the substrate envelope of SARS-CoV-2 main protease to predict and avoid drug resistance.
Nat Commun, 13, 2022
7MB9
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SARS-CoV-2 Main Protease (Mpro) C145A in Complex with Cleavage Site Nsp10/11 (P6-P1)
Descriptor: 3C-like proteinase, ARG-GLU-PRO-MET-LEU-GLN
Authors:Lockbaum, G.J, Schiffer, C.A.
Deposit date:2021-03-31
Release date:2022-06-22
Last modified:2023-10-18
Method:X-RAY DIFFRACTION (1.81 Å)
Cite:Defining the substrate envelope of SARS-CoV-2 main protease to predict and avoid drug resistance.
Nat Commun, 13, 2022
7T70
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BU of 7t70 by Molmil
Co-crystal structure of SARS-CoV-2 Mpro C145A with substrate peptide 4/5
Descriptor: 3C-like proteinase, DIMETHYL SULFOXIDE, GLYCEROL, ...
Authors:Shaqra, A.M, Schiffer, C.A.
Deposit date:2021-12-14
Release date:2022-06-22
Last modified:2023-10-18
Method:X-RAY DIFFRACTION (2.35 Å)
Cite:Defining the substrate envelope of SARS-CoV-2 main protease to predict and avoid drug resistance.
Nat Commun, 13, 2022
7T8M
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BU of 7t8m by Molmil
Co-crystal structure of SARS-CoV-2 Mpro C145A with substrate peptide 5/6
Descriptor: 3C-like proteinase, DIMETHYL SULFOXIDE, GLYCEROL, ...
Authors:Shaqra, A.M, Schiffer, C.A.
Deposit date:2021-12-16
Release date:2022-06-22
Last modified:2023-10-18
Method:X-RAY DIFFRACTION (1.6 Å)
Cite:Defining the substrate envelope of SARS-CoV-2 main protease to predict and avoid drug resistance.
Nat Commun, 13, 2022
7T8R
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BU of 7t8r by Molmil
Co-crystal structure of SARS-CoV-2 Mpro C145A with substrate peptide 7/8
Descriptor: 1,2-ETHANEDIOL, 3C-like proteinase, GLYCEROL, ...
Authors:Shaqra, A.M, Schiffer, C.A.
Deposit date:2021-12-16
Release date:2022-06-22
Last modified:2023-10-18
Method:X-RAY DIFFRACTION (1.74 Å)
Cite:Defining the substrate envelope of SARS-CoV-2 main protease to predict and avoid drug resistance.
Nat Commun, 13, 2022
7T9Y
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BU of 7t9y by Molmil
Co-crystal structure of SARS-CoV-2 Mpro C145A with substrate peptide 8/9
Descriptor: 3C-like proteinase, GLYCEROL, Nonstructural protein 8/9
Authors:Shaqra, A.M, Schiffer, C.A.
Deposit date:2021-12-20
Release date:2022-06-22
Last modified:2023-10-18
Method:X-RAY DIFFRACTION (2.18 Å)
Cite:Defining the substrate envelope of SARS-CoV-2 main protease to predict and avoid drug resistance.
Nat Commun, 13, 2022
7TA4
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BU of 7ta4 by Molmil
Co-crystal structure of SARS-CoV-2 Mpro C145A with substrate peptide 9/10
Descriptor: 3C-like proteinase, Nonstructural protein 9/10
Authors:Shaqra, A.M, Schiffer, C.A.
Deposit date:2021-12-20
Release date:2022-06-22
Last modified:2023-10-18
Method:X-RAY DIFFRACTION (1.78 Å)
Cite:Defining the substrate envelope of SARS-CoV-2 main protease to predict and avoid drug resistance.
Nat Commun, 13, 2022
7TA7
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BU of 7ta7 by Molmil
Co-crystal structure of SARS-CoV-2 Mpro C145A with substrate peptide 10/11
Descriptor: 3C-like proteinase, GLYCEROL, Nonstructural protein 10/11
Authors:Shaqra, A.M, Schiffer, C.A.
Deposit date:2021-12-20
Release date:2022-06-22
Last modified:2023-10-18
Method:X-RAY DIFFRACTION (2.28 Å)
Cite:Defining the substrate envelope of SARS-CoV-2 main protease to predict and avoid drug resistance.
Nat Commun, 13, 2022
7TB2
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BU of 7tb2 by Molmil
Co-crystal structure of SARS-CoV-2 Mpro C145A with substrate peptide 12/13
Descriptor: 3C-like proteinase, Nonstructural protein 12/13
Authors:Shaqra, A.M, Schiffer, C.A.
Deposit date:2021-12-21
Release date:2022-06-22
Last modified:2023-10-18
Method:X-RAY DIFFRACTION (1.8 Å)
Cite:Defining the substrate envelope of SARS-CoV-2 main protease to predict and avoid drug resistance.
Nat Commun, 13, 2022
7TBT
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BU of 7tbt by Molmil
Co-crystal structure of SARS-CoV-2 Mpro C145A with substrate peptide 13/14
Descriptor: 3C-like proteinase, Nonstructural protein 13/14
Authors:Shaqra, A.M, Schiffer, C.A.
Deposit date:2021-12-22
Release date:2022-06-22
Last modified:2023-10-18
Method:X-RAY DIFFRACTION (2.45 Å)
Cite:Defining the substrate envelope of SARS-CoV-2 main protease to predict and avoid drug resistance.
Nat Commun, 13, 2022
7TC4
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BU of 7tc4 by Molmil
Co-crystal structure of SARS-CoV-2 Mpro C145A with substrate peptide 15/16
Descriptor: 3C-like proteinase, GLYCEROL, Nonstructural protein 15/16
Authors:Shaqra, A.M, Schiffer, C.A.
Deposit date:2021-12-22
Release date:2022-06-22
Last modified:2023-10-18
Method:X-RAY DIFFRACTION (1.94 Å)
Cite:Defining the substrate envelope of SARS-CoV-2 main protease to predict and avoid drug resistance.
Nat Commun, 13, 2022
7TQ2
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BU of 7tq2 by Molmil
Structure of SARS-CoV-2 3CL protease in complex with the cyclopropane based inhibitor 1c
Descriptor: 3C-like proteinase, N-{(2S)-1-oxo-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-N~2~-({[(1R,2R)-2-phenylcyclopropyl]methoxy}carbonyl)-L-leucinamide
Authors:Lovell, S, Kashipathy, M.M, Battaile, K.P, Nguyen, H.N, Chamandi, S.D, Picard, H.R, Madden, T.K, Thruman, H.A, Kim, Y, Groutas, W.C, Chang, K.O.
Deposit date:2022-01-26
Release date:2022-06-22
Last modified:2023-10-25
Method:X-RAY DIFFRACTION (2.3 Å)
Cite:Broad-Spectrum Cyclopropane-Based Inhibitors of Coronavirus 3C-like Proteases: Biochemical, Structural, and Virological Studies.
Acs Pharmacol Transl Sci, 6, 2023
7TQ3
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BU of 7tq3 by Molmil
Structure of SARS-CoV-2 3CL protease in complex with the cyclopropane based inhibitor 5c
Descriptor: 3C-like proteinase, N~2~-({[(1R,2R)-2-(3-fluorophenyl)cyclopropyl]methoxy}carbonyl)-N-{(2S)-1-oxo-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-L-leucinamide
Authors:Lovell, S, Battaile, K.P, Nguyen, H.N, Chamandi, S.D, Picard, H.R, Madden, T.K, Thruman, H.A, Kim, Y, Groutas, W.C, Chang, K.O.
Deposit date:2022-01-26
Release date:2022-06-22
Last modified:2023-10-25
Method:X-RAY DIFFRACTION (2 Å)
Cite:Broad-Spectrum Cyclopropane-Based Inhibitors of Coronavirus 3C-like Proteases: Biochemical, Structural, and Virological Studies.
Acs Pharmacol Transl Sci, 6, 2023
7TQ4
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BU of 7tq4 by Molmil
Structure of SARS-CoV-2 3CL protease in complex with the cyclopropane based inhibitor 6c
Descriptor: 3C-like proteinase, N~2~-({[(1R,2R)-2-(3-chlorophenyl)cyclopropyl]methoxy}carbonyl)-N-{(2S)-1-oxo-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-L-leucinamide
Authors:Lovell, S, Battaile, K.P, Nguyen, H.N, Chamandi, S.D, Picard, H.R, Madden, T.K, Thruman, H.A, Kim, Y, Groutas, W.C, Chang, K.O.
Deposit date:2022-01-26
Release date:2022-06-22
Last modified:2023-10-25
Method:X-RAY DIFFRACTION (2.45 Å)
Cite:Broad-Spectrum Cyclopropane-Based Inhibitors of Coronavirus 3C-like Proteases: Biochemical, Structural, and Virological Studies.
Acs Pharmacol Transl Sci, 6, 2023
7UXX
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BU of 7uxx by Molmil
Crystal structure of SARS-CoV-2 nucleocapsid protein C-terminal domain
Descriptor: ACETATE ION, GLYCEROL, Nucleoprotein
Authors:Bezerra, E.H.S, Tonoli, C.C.C, Soprano, A.S, Franchini, K.G, Trivella, D.B.B, Benedetti, C.E.
Deposit date:2022-05-06
Release date:2022-06-22
Last modified:2023-10-18
Method:X-RAY DIFFRACTION (1.85 Å)
Cite:Discovery and structural characterization of chicoric acid as a SARS-CoV-2 nucleocapsid protein ligand and RNA binding disruptor.
Sci Rep, 12, 2022
7UXZ
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BU of 7uxz by Molmil
Crystal structure of SARS-CoV-2 nucleocapsid protein C-terminal domain complexed with Chicoric acid
Descriptor: (2R,3R)-2,3-bis{[(2E)-3-(3,4-dihydroxyphenyl)prop-2-enoyl]oxy}butanedioic acid, CHLORIDE ION, DI(HYDROXYETHYL)ETHER, ...
Authors:Bezerra, E.H.S, Tonoli, C.C.C, Soprano, A.S, Franchini, K.G, Trivella, D.B.B, Benedetti, C.E.
Deposit date:2022-05-06
Release date:2022-06-22
Last modified:2023-10-18
Method:X-RAY DIFFRACTION (1.733 Å)
Cite:Discovery and structural characterization of chicoric acid as a SARS-CoV-2 nucleocapsid protein ligand and RNA binding disruptor.
Sci Rep, 12, 2022
7V61
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BU of 7v61 by Molmil
ACE2 -Targeting Monoclonal Antibody as Potent and Broad-Spectrum Coronavirus Blocker
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, 3E8, ...
Authors:Yan, R.H, Zhang, Y.Y, Li, Y.N, Zhou, Q.
Deposit date:2021-08-18
Release date:2022-06-22
Method:ELECTRON MICROSCOPY (3.2 Å)
Cite:ACE2-targeting monoclonal antibody as potent and broad-spectrum coronavirus blocker.
Signal Transduct Target Ther, 6, 2021
7VRV
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BU of 7vrv by Molmil
VAS5 Spike (1 RBD up)
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:Zhen, C, Wang, X.
Deposit date:2021-10-25
Release date:2022-06-22
Method:ELECTRON MICROSCOPY (4.2 Å)
Cite:VAS5 Spike(1 RBD up)
To Be Published
7VRW
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VAS5 Spike (3 RBD down)
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:Zhen, C, Wang, X.
Deposit date:2021-10-25
Release date:2022-06-22
Method:ELECTRON MICROSCOPY (3.6 Å)
Cite:VAS5 Spike (3-RBD down)
To Be Published

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數據於2024-07-10公開中

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