7CUT

Crystal structure of the SARS-CoV-2 (COVID-19) main protease in complex with Z-VAD-FMK

PDB DOI: https://doi.org/10.2210/pdb7CUT/pdb

Classification: VIRAL PROTEIN
Organism(s): Severe acute respiratory syndrome coronavirus 2, synthetic construct
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2020-08-24 Released: 2021-06-23
Deposition Author(s): Lu, M., Yang, H.T., Wang, Z.Y., Zhao, Y., Xing, Y.F.
Funding Organization(s): National Natural Science Foundation of China (NSFC), Other government

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.82 Å
R-Value Free: 0.223
R-Value Work: 0.182
R-Value Observed: 0.185

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

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

Literature

Identification of proteasome and caspase inhibitors targeting SARS-CoV-2 M pro .

Wang, Z., Zhao, Y., Wang, Q., Xing, Y., Feng, L., Kong, J., Peng, C., Zhang, L., Yang, H., Lu, M.

(2021) Signal Transduct Target Ther 6: 214-214

PubMed: 34075025 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1038/s41392-021-00639-8
Primary Citation of Related Structures:
7CUT, 7CUU

Organizational Affiliation

Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine (Shanghai), Ruijin Hospital affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China.

Macromolecule Content

Total Structure Weight: 34.67 kDa
Atom Count: 2,562
Modelled Residue Count: 306
Deposited Residue Count: 311
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3C protein	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% Identity50% Identity70% Identity90% Identity95% Identity100% 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	5	synthetic construct	Mutation(s): 0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A]	D [auth A], E [auth A], F [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A]
DMS Query on DMS 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]	DIMETHYL SULFOXIDE C₂ H₆ O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N		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	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	Z-VAD(OMe)-FMK	Peptide-like / Inhibitor		Interactions Focus chain B Interactions & Density Focus chain B

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.82 Å
R-Value Free: 0.223
R-Value Work: 0.182
R-Value Observed: 0.185
Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 98.22	α = 90
b = 82.65	β = 115.28
c = 51.74	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XSCALE	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
Coot	model building

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2021-06-23

Deposition Author(s):

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	81520108019
National Natural Science Foundation of China (NSFC)	China	813300237
Other government	China	Clinical Research Program of Ruijin Hospital (2018CR006)
Other government	China	Shanghai Youth Talent Development Program (2017275)
Other government	China	Shanghai Medical and Health Excellent Discipline Leader Development Plan (2018BR36)
Other government	China	Shanghai Collaborative Innovation Center for Translational Medicine (TM201902)
Other government	China	Foundation of National Facility for Translational Medicine (Shanghai) (TMSK-2020-003)

Revision History (Full details and data files)

Version 1.0: 2021-06-23
Type: Initial release
Version 1.1: 2021-07-07
Changes: Database references
Version 1.2: 2023-11-29
Changes: Data collection, Database references, Derived calculations, Refinement description