Crystal structure of the SARS-CoV-2 main protease in complex with Z-VAD(OMe)-FMK
Qiao, J.X., Zeng, R., Wang, Y.F., Li, Y.S., Yao, R., Zhou, Y.L., Chen, P., Lei, J., Yang, S.Y.To be published.
Experimental Data Snapshot
wwPDB Validation   3D Report Full Report
Entity ID: 1 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
3C-like proteinase | 306 | Severe acute respiratory syndrome coronavirus 2 | Mutation(s): 0  Gene Names: rep, 1a-1b EC: 3.4.22.69 | ||
UniProt | |||||
Find proteins for P0DTD1 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTD1  Go to UniProtKB:  P0DTD1 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P0DTD1 | ||||
Sequence AnnotationsExpand | |||||
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Find similar proteins by: Sequence | 3D Structure
Entity ID: 2 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
Z-VAD(OMe)-FMK | B [auth D] | 5 | synthetic construct | Mutation(s): 0  | |
Sequence AnnotationsExpand | |||||
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Ligands 1 Unique | |||||
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ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
CL (Subject of Investigation/LOI) Query on CL | C [auth A] | CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M |
Modified Residues 1 Unique | |||||
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ID | Chains | Type | Formula | 2D Diagram | Parent |
FL6 Query on FL6 | B [auth D] | L-PEPTIDE LINKING | C5 H9 N O4 | ASP |
Entity ID: 2 | |||||
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ID | Chains | Name | Type/Class | 2D Diagram | 3D Interactions |
PRD_002352 Query on PRD_002352 | B [auth D] | Z-VAD(OMe)-FMK | Peptide-like / Inhibitor |
Length ( Å ) | Angle ( ˚ ) |
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a = 98.26 | α = 90 |
b = 82.3 | β = 115.58 |
c = 51.765 | γ = 90 |
Software Name | Purpose |
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REFMAC | refinement |
PDB_EXTRACT | data extraction |
XDS | data reduction |
Aimless | data scaling |
MOLREP | phasing |
Funding Organization | Location | Grant Number |
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National Natural Science Foundation of China (NSFC) | China | 2020YFS0010/HX2019nCoV039 |