7C8B | pdb_00007c8b

Crystal structure of the SARS-CoV-2 main protease in complex with Z-VAD(OMe)-FMK

PDB DOI: https://doi.org/10.2210/pdb7C8B/pdb

Classification: HYDROLASE/HYDROLASE INHIBITOR
Organism(s): Severe acute respiratory syndrome coronavirus 2, synthetic construct
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2020-05-29 Released: 2020-09-02
Deposition Author(s): Zeng, R., Qiao, J.X., Wang, Y.F., Li, Y.S., Yao, R., Yang, S.Y., Lei, J.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free:
0.230 (Depositor), 0.216 (DCC)
R-Value Work:
0.177 (Depositor)
R-Value Observed:
0.179 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

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.

Macromolecule Content

Total Structure Weight: 34.35 kDa
Atom Count: 2,606
Modeled Residue Count: 306
Deposited Residue Count: 311
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3C-like proteinase	A	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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0DTD1
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Z-VAD(OMe)-FMK	B [auth D]	5	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CL (Subject of Investigation/LOI) Query on CL Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
FL6 Query on FL6	B [auth D]	L-PEPTIDE LINKING	C₅ H₉ N O₄		ASP

Biologically Interesting Molecules (External Reference)

1 Unique

Entity ID: 2
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		Interactions Focus chain B [auth D] Interactions & Density Focus chain B [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.230 (Depositor), 0.216 (DCC)
R-Value Work: 0.177 (Depositor)
R-Value Observed: 0.179 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 98.26	α = 90
b = 82.3	β = 115.58
c = 51.765	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
Aimless	data scaling
MOLREP	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2020-09-02

Deposition Author(s):

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	2020YFS0010/HX2019nCoV039

Revision History (Full details and data files)

Version 1.0: 2020-09-02
Type: Initial release
Version 1.1: 2021-03-10
Changes: Structure summary
Version 1.2: 2023-11-29
Changes: Advisory, Data collection, Database references, Derived calculations, Refinement description