5QH9

PanDDA analysis group deposition of models with modelled events (e.g. bound ligands) -- Crystal Structure of NUDT7 in complex with PCM-0102716


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.72 Å
  • R-Value Free: 
    0.206 (Depositor), 0.210 (DCC) 
  • R-Value Work: 
    0.183 (Depositor), 0.190 (DCC) 
  • R-Value Observed: 
    0.185 (Depositor) 

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 GZYClick on this verticalbar to view details

This is version 1.1 of the entry. See complete history


Literature

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Peroxisomal coenzyme A diphosphatase NUDT7196Homo sapiensMutation(s): 0 
Gene Names: NUDT7
EC: 3.6.1 (PDB Primary Data), 3.6.1.77 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P0C024 (Homo sapiens)
Explore P0C024 
Go to UniProtKB:  P0C024
PHAROS:  P0C024
GTEx:  ENSG00000140876 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0C024
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Modified Residues  2 Unique
IDChains TypeFormula2D DiagramParent
CSO
Query on CSO
A
L-PEPTIDE LINKINGC3 H7 N O3 SCYS
HYP
Query on HYP
A
L-PEPTIDE LINKINGC5 H9 N O3PRO
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.72 Å
  • R-Value Free:  0.206 (Depositor), 0.210 (DCC) 
  • R-Value Work:  0.183 (Depositor), 0.190 (DCC) 
  • R-Value Observed: 0.185 (Depositor) 
Space Group: P 3 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 124.671α = 90
b = 124.671β = 90
c = 41.174γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
REFMACphasing

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 GZYClick on this verticalbar to view details

Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2019-03-27
    Type: Initial release
  • Version 1.1: 2023-11-15
    Changes: Data collection, Database references