7TWV

Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with ADP-ribose at pH 5 (P43 crystal form)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.90 Å
  • R-Value Free: 0.107 
  • R-Value Work: 0.095 
  • R-Value Observed: 0.096 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with ADP-ribose at pH 5 (P43 crystal form)

Correy, G.J.Fraser, J.S.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Non-structural protein 3
A, B
169Severe acute respiratory syndrome coronavirus 2Mutation(s): 0 
Gene Names: rep1a-1b
EC: 3.4.22
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 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
AR6 (Subject of Investigation/LOI)
Query on AR6

Download Ideal Coordinates CCD File 
C [auth A][(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL [HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL] HYDROGEN PHOSPHATE
C15 H23 N5 O14 P2
SRNWOUGRCWSEMX-ZQSHOCFMSA-N
CIT
Query on CIT

Download Ideal Coordinates CCD File 
D [auth A],
E [auth B]
CITRIC ACID
C6 H8 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.90 Å
  • R-Value Free: 0.107 
  • R-Value Work: 0.095 
  • R-Value Observed: 0.096 
  • Space Group: P 43
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 88.393α = 90
b = 88.393β = 90
c = 39.924γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
PHENIXrefinement
XDSdata scaling
PHASERphasing
Cootmodel building

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesGM123159
National Science Foundation (NSF, United States)United States2031205

Revision History  (Full details and data files)

  • Version 1.0: 2022-02-23
    Type: Initial release
  • Version 1.1: 2023-10-18
    Changes: Data collection, Refinement description