5UQ9

Crystal structure of 6-phosphogluconate dehydrogenase with ((4R,5R)-5-(hydroxycarbamoyl)-2,2-dimethyl-1,3-dioxolan-4-yl)methyl dihydrogen phosphate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.217 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
6-phosphogluconate dehydrogenase, decarboxylating
A, B, C, D, E, F, G, H
489Homo sapiensMutation(s): 0 
Gene Names: PGD (PGDH)
EC: 1.1.1.44
Find proteins for P52209 (Homo sapiens)
Go to Gene View: PGD
Go to UniProtKB:  P52209
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
8HS
Query on 8HS

Download SDF File 
Download CCD File 
F
[(4R,5R)-5-(hydroxycarbamoyl)-2,2-dimethyl-1,3-dioxolan-4-yl]methyl dihydrogen phosphate
C7 H14 N O8 P
DVFAQEVWJBLFDS-RFZPGFLSSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.217 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 87.311α = 90.00
b = 164.930β = 91.43
c = 133.199γ = 90.00
Software Package:
Software NamePurpose
Aimlessdata scaling
PHASERphasing
PHENIXrefinement
iMOSFLMdata reduction
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2017-02-07 
  • Released Date: 2018-08-22 
  • Deposition Author(s): Leonard, P.G.

Revision History 

  • Version 1.0: 2018-08-22
    Type: Initial release
  • Version 1.1: 2019-01-23
    Type: Data collection, Database references