4GWG Oxidoreductase date Sep 03, 2012
title Crystal Structure Analysis Of 6-Phosphogluconate Dehydrogena Form
authors C.He, L.Zhou, L.Zhang
compound source
Molecule: 6-Phosphogluconate Dehydrogenase, Decarboxylating
Chain: A
Ec: 1.1.1.44
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Pgd, Pgdh
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: P 43 21 2
R_factor 0.169 R_Free 0.186
crystal
cell
length a length b length c angle alpha angle beta angle gamma
87.280 87.280 130.892 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.39 Å
ligand MES enzyme Oxidoreductase E.C.1.1.1.44 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referencePhosphoglycerate mutase 1 coordinates glycolysis and biosynthesis to promote tumor growth., Hitosugi T, Zhou L, Elf S, Fan J, Kang HB, Seo JH, Shan C, Dai Q, Zhang L, Xie J, Gu TL, Jin P, Aleckovic M, Leroy G, Kang Y, Sudderth JA, Deberardinis RJ, Luan CH, Chen GZ, Muller S, Shin DM, Owonikoko TK, Lonial S, Arellano ML, Khoury HJ, Khuri FR, Lee BH, Ye K, Boggon TJ, Kang S, He C, Chen J, Cancer Cell. 2012 Nov 13;22(5):585-600. doi: 10.1016/j.ccr.2012.09.020. PMID:23153533
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (91 Kb) [Save to disk]
  • Biological Unit Coordinates (4gwg.pdb1.gz) 87 Kb
  • Biological Unit Coordinates (4gwg.pdb2.gz) 172 Kb
  • LPC: Ligand-Protein Contacts for 4GWG
  • CSU: Contacts of Structural Units for 4GWG
  • Structure Factors (3624 Kb)
  • Retrieve 4GWG in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4GWG from S2C, [Save to disk]
  • Re-refined 4gwg structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4GWG in 3D
  • Proteopedia, because life has more than 2D.
  • On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.
  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
  • Visual 3D analysis of 4GWG
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 4GWG, from MSDmotif at EBI
  • Fold representative 4gwg from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4gwg_A] [4gwg]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 4GWG: [6PGD ] by SMART
  • Other resources with information on 4GWG
  • Community annotation for 4GWG at PDBWiki (http://pdbwiki.org)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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