2JKV

Structure of human Phosphogluconate Dehydrogenase in complex with NADPH at 2.53A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.532 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.156 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structure of Human Phosphogluconate Dehydrogenase in Complex with Nadph at 2.53A

Ng, S.S.von Delft, F.Pilka, E.S.Kavanagh, K.L.McDonough, M.A.Savitsky, P.Arrowsmith, C.H.Weigelt, J.Edwards, A.Sundstrom, M.Schofield, C.J.Oppermann, U.

To be published.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
6-PHOSPHOGLUCONATE DEHYDROGENASE, DECARBOXYLATING
A, B, C, D, E, F
505Homo 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 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B, C, D, E, F
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
CL
Query on CL

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Download CCD File 
A, B, D, E, F
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
NAP
Query on NAP

Download SDF File 
Download CCD File 
A, B, C, D, E
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE
C21 H28 N7 O17 P3
XJLXINKUBYWONI-NNYOXOHSSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.532 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.156 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 56.643α = 90.00
b = 204.714β = 90.65
c = 170.319γ = 90.00
Software Package:
Software NamePurpose
MOSFLMdata reduction
PHENIXrefinement
SCALAdata scaling
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-09-01
    Type: Initial release
  • Version 1.1: 2015-01-14
    Type: Atomic model, Database references, Derived calculations, Non-polymer description, Other, Refinement description, Structure summary, Version format compliance
  • Version 1.2: 2018-01-24
    Type: Database references
  • Version 1.3: 2018-02-21
    Type: Database references