7MHP

Ensemble refinement structure of SARS-CoV-2 main protease (Mpro) at 298 K at high humidity


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.159 
  • R-Value Observed: 0.163 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 2.2 of the entry. See complete history


Literature

The temperature-dependent conformational ensemble of SARS-CoV-2 main protease (M pro )

Ebrahim, A.Riley, B.T.Kumaran, D.Andi, B.Fuchs, M.R.McSweeney, S.Keedy, D.A.

(2022) IUCrJ 9: 682-694


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
3C-like proteinase306Severe acute respiratory syndrome coronavirus 2Mutation(s): 0 
Gene Names: rep1a-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 Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0DTD1
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download Ideal Coordinates CCD File 
B [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.159 
  • R-Value Observed: 0.163 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 114.88α = 90
b = 54.736β = 101.42
c = 45.24γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
xia2data reduction
DIALSdata scaling
PHASERphasing
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM133769
Department of Energy (DOE, United States)United StatesNational Virtual Biotechnology Laboratory (NVBL)
Department of Energy (DOE, United States)United StatesCoronavirus CARES Act
Department of Energy (DOE, United States)United StatesBNL LDRD 20-042
Department of Energy (DOE, United States)United StatesDE-SC0012704
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesP30GM133893
Department of Energy (DOE, United States)United StatesKP1605010

Revision History  (Full details and data files)

  • Version 1.0: 2021-05-12
    Type: Initial release
  • Version 1.1: 2021-05-26
    Changes: Database references
  • Version 2.0: 2022-04-06
    Type: Coordinate replacement
    Reason: Ligand identity
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Refinement description, Source and taxonomy, Structure summary
  • Version 2.1: 2022-09-07
    Changes: Database references
  • Version 2.2: 2023-10-18
    Changes: Data collection, Refinement description