2JKV

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.53 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.156 
  • R-Value Observed: 0.157 

Starting Models: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.4 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
6-PHOSPHOGLUCONATE DEHYDROGENASE, DECARBOXYLATING
A, B, C, D, E
A, B, C, D, E, F
505Homo sapiensMutation(s): 0 
EC: 1.1.1.44
UniProt & NIH Common Fund Data Resources
Find proteins for P52209 (Homo sapiens)
Explore P52209 
Go to UniProtKB:  P52209
PHAROS:  P52209
GTEx:  ENSG00000142657 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP52209
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAP
Query on NAP

Download Ideal Coordinates CCD File 
G [auth A],
M [auth B],
S [auth C],
V [auth D],
Z [auth E]
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H28 N7 O17 P3
XJLXINKUBYWONI-NNYOXOHSSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
AA [auth E]
BA [auth E]
FA [auth F]
GA [auth F]
I [auth A]
AA [auth E],
BA [auth E],
FA [auth F],
GA [auth F],
I [auth A],
J [auth A],
P [auth B],
Q [auth B],
T [auth C],
U [auth C],
W [auth D],
X [auth D]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
CL
Query on CL

Download Ideal Coordinates CCD File 
CA [auth E]
DA [auth E]
EA [auth F]
H [auth A]
HA [auth F]
CA [auth E],
DA [auth E],
EA [auth F],
H [auth A],
HA [auth F],
K [auth A],
L [auth A],
N [auth B],
O [auth B],
R [auth B],
Y [auth D]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.53 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.156 
  • R-Value Observed: 0.157 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 56.643α = 90
b = 204.714β = 90.65
c = 170.319γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2009-09-01
    Type: Initial release
  • Version 1.1: 2015-01-14
    Changes: Atomic model, Database references, Derived calculations, Non-polymer description, Other, Refinement description, Structure summary, Version format compliance
  • Version 1.2: 2018-01-24
    Changes: Database references
  • Version 1.3: 2018-02-21
    Changes: Database references
  • Version 1.4: 2023-12-13
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description