6Z2E

Crystal structure of SARS-CoV-2 Mpro in complex with the activity-based probe, biotin-PEG(4)-Abu-Tle-Leu-Gln-vinylsulfone


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 
    0.243 (Depositor), 0.250 (DCC) 
  • R-Value Work: 
    0.192 (Depositor), 0.200 (DCC) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted Q5TClick on this verticalbar to view details

This is version 1.3 of the entry. See complete history


Literature

Crystal structure of SARS-CoV-2 Mpro in complex with the activity-based probe, biotin-PEG(4)-Abu-Tle-Leu-Gln-vinylsulfone

Zhang, L.Hilgenfeld, R.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
3C-like proteinaseA [auth AAA]306Severe 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 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Q5T (Subject of Investigation/LOI)
Query on Q5T

Download Ideal Coordinates CCD File 
B [auth AAA](4~{S})-4-[[(2~{S})-2-[[(2~{S})-2-[[(2~{S})-2-[3-[2-[2-[2-[2-[5-[(3~{a}~{S},4~{R},6~{a}~{R})-2-oxidanylidene-3,3~{a},4,6~{a}-tetrahydro-1~{H}-thieno[3,4-d]imidazol-4-yl]pentanoylamino]ethoxy]ethoxy]ethoxy]ethoxy]propanoylamino]butanoyl]amino]-3,3-dimethyl-butanoyl]amino]-4-methyl-pentanoyl]amino]-6-methylsulfonyl-hexanamide
C44 H80 N8 O13 S2
GNJWOJZWTQAVJG-ZFKAINLFSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
C [auth AAA],
D [auth AAA]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA
Query on NA

Download Ideal Coordinates CCD File 
E [auth AAA]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free:  0.243 (Depositor), 0.250 (DCC) 
  • R-Value Work:  0.192 (Depositor), 0.200 (DCC) 
Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 104.083α = 90
b = 104.083β = 90
c = 91.246γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted Q5TClick on this verticalbar to view details

Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Union (EU)Germany# 101003627

Revision History  (Full details and data files)

  • Version 1.0: 2020-06-17
    Type: Initial release
  • Version 1.1: 2021-04-28
    Changes: Source and taxonomy, Structure summary
  • Version 1.2: 2024-01-24
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.3: 2024-10-23
    Changes: Structure summary