5QHF

PanDDA analysis group deposition of models with modelled events (e.g. bound ligands) -- Crystal Structure of NUDT7 in complex with NUOOA000301a


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.67 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.194 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Peroxisomal coenzyme A diphosphatase NUDT7
A
196Homo sapiensMutation(s): 0 
Gene Names: NUDT7
EC: 3.6.1.-
Find proteins for P0C024 (Homo sapiens)
Go to Gene View: NUDT7
Go to UniProtKB:  P0C024
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
H1G
Query on H1G

Download SDF File 
Download CCD File 
A
2-(4-methoxyphenyl)-N-{5-[2-oxo-2-(3-oxopiperazin-1-yl)ethoxy]pyridin-3-yl}acetamide
C20 H22 N4 O5
HQORDXPKFUZBKB-UHFFFAOYSA-N
 Ligand Interaction
ACT
Query on ACT

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Download CCD File 
A
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
DMS
Query on DMS

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Download CCD File 
A
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D 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: 1.67 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.194 
  • Space Group: P 3 2 1
Unit Cell:
Length (Å)Angle (°)
a = 124.659α = 90.00
b = 124.659β = 90.00
c = 41.113γ = 120.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
XDSdata reduction
REFMACphasing
REFMACrefinement
Aimlessdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Revision History 

  • Version 1.0: 2019-03-27
    Type: Initial release