7VK8 | pdb_00007vk8

Crystal structure of SARS-CoV-2 Mpro at 2.4 A Resolution

PDB DOI: https://doi.org/10.2210/pdb7VK8/pdb

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

Deposited: 2021-09-29 Released: 2022-01-26
Deposition Author(s): DeMirci, H., Usta, G.
Funding Organization(s): National Science Foundation (NSF, United States), Other government

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free:
0.329 (Depositor), 0.334 (DCC)
R-Value Work:
0.272 (Depositor), 0.274 (DCC)
R-Value Observed:
0.278 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.1 of the entry. See complete history.

Literature

Case Study of High-Throughput Drug Screening and Remote Data Collection for SARS-CoV-2 Main Protease by Using Serial Femtosecond X-ray Crystallography

Guven, O., Gul, M., Ayan, E., Johnson, J.A., Cakilkaya, B., Usta, G., Ertem, F.B., Tokay, N., Yuksel, B., Gocenler, O., Buyukdag, C., Botha, S., Ketawala, G., Su, Z., Hayes, B., Poitevin, F., Batyuk, A., Yoon, C.H., Kupitz, C., Durdagi, S., Sierra, R.G., DeMirci, H.

(2021) Crystals (Basel) 11

DOI: https://doi.org/10.3390/cryst11121579

Macromolecule Content

Total Structure Weight: 33.83 kDa
Atom Count: 2,502
Modeled Residue Count: 305
Deposited Residue Count: 306
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3C-like proteinase	A	306	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0 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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.329 (Depositor), 0.334 (DCC)
R-Value Work: 0.272 (Depositor), 0.274 (DCC)
R-Value Observed: 0.278 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 115.3	α = 90
b = 55.2	β = 101.3
c = 45.7	γ = 90

Software Package:

Software Name	Purpose
Aimless	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
CrystFEL	data reduction
PHASER	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2022-01-26

Deposition Author(s):

Funding Organization	Location	Grant Number
National Science Foundation (NSF, United States)	United States	NSF-1231306
Other government	Turkey	118C260

Revision History (Full details and data files)

Version 1.0: 2022-01-26
Type: Initial release
Version 1.1: 2023-11-29
Changes: Data collection, Refinement description

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.