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 
  • R-Value Work: 0.192 

Starting Model: experimental
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Ligand Structure Quality Assessment 


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
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Q5T (Subject of Investigation/LOI)
Query on Q5T

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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

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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 
  • R-Value Work: 0.192 
  • 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

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Ligand Structure Quality Assessment 


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