4GWK Oxidoreductase date Sep 03, 2012
title Crystal Structure Of 6-Phosphogluconate Dehydrogenase Comple 3-Phosphoglyceric Acid
authors C.He, L.Zhou, L.Zhang
compound source
Molecule: 6-Phosphogluconate Dehydrogenase, Decarboxylating
Chain: A
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 0.170 R_Free 0.174
length a length b length c angle alpha angle beta angle gamma
87.246 87.246 130.424 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.53 Å
ligand 3PG, MES enzyme Oxidoreductase E.C. BRENDA

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] (89 Kb) [Save to disk]
  • Biological Unit Coordinates (4gwk.pdb1.gz) 84 Kb
  • Biological Unit Coordinates (4gwk.pdb2.gz) 165 Kb
  • LPC: Ligand-Protein Contacts for 4GWK
  • CSU: Contacts of Structural Units for 4GWK
  • Structure Factors (2482 Kb)
  • Retrieve 4GWK in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4GWK from S2C, [Save to disk]
  • Re-refined 4gwk structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4GWK 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 4GWK
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Electron Density related parameters from EDS Electron Density Server, at Upsala
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 4GWK, from MSDmotif at EBI
  • Fold representative 4gwk from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4gwk_A] [4gwk]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 4GWK: [6PGD ] by SMART
  • Other resources with information on 4GWK
  • Community annotation for 4GWK at PDBWiki (http://pdbwiki.org)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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