2JKV

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

Structural Biology Knowledgebase: 2JKV SBKB.org


Experimental Data Snapshot

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

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 2JKV

Classification: OXIDOREDUCTASE

Total Structure Weight: 339844.92

Macromolecule Entities
Molecule Chains Length Organism Details
6-PHOSPHOGLUCONATE DEHYDROGENASE, DECARBOXYLATING A, B, C..., D, E, FA, B, C, D, E, F 505 Homo sapiens EC#: 1.1.1.44 IUBMB
Gene Name(s): PGD Gene View PGDH

Small Molecules
Ligands 3 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
NAP
Query on NAP

A, B, C, D, E NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE (Synonym)
C21 H28 N7 O17 P3
XJLXINKUBYWONI-NNYOXOHSSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SO4
Query on SO4

A, B, C, D, E, F SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CL
Query on CL

A, B, D, E, F CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.53 Å
  • R-Value Free: 0.207
  • R-Value Work: 0.156
  • Space Group: P 1 21 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 56.64 α = 90.00
b = 204.71 β = 90.65
c = 170.32 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2008-09-01
  • Released Date: 2009-09-01
  • Deposition author(s): Pilka, E.S., Kavanagh, K.L., von Delft, F., Muniz, J.R.C., Murray, J., Picaud, S., Guo, K., Edwards, A., Arrowsmith, C.H., Weigelt, J., Bountra, C., Oppermann, U.

Revision History

  • 2015-01-14
    Type: Function and keywords | Details: KEYWDS
  • 2015-01-14
    Type: Linkage | Details: CONECT
  • 2015-01-14
    Type: Biological assembly | Details: REMARK 300,REMARK 350
  • 2015-01-14
    Type: Atom nomenclature | Details: ATOM,HETATM
  • 2015-01-14
    Type: Other | Details: ANISOU,REMARK 465,TER,MASTER
  • 2015-01-14
    Type: Refinement description | Details: REMARK 3
  • 2015-01-14
    Type: Entry authorship | Details: AUTHOR
  • 2015-01-14
    Type: Polymer description | Details: COMPND
  • 2015-01-14
    Type: Version format compliance | Details: REMARK 4
  • 2015-01-14
    Type: Geometry validation | Details: REMARK 500
  • 2015-01-14
    Type: Non-polymer description | Details: HETSYN,FORMUL
  • 2015-01-14
    Type: Binding sites and description | Details: SITE
  • 2015-01-14
    Type: Citation | Details: JRNL
  • 2015-01-14
    Type: Secondary structure | Details: HELIX,SHEET