2PGD Oxidoreductase (Choh(D)-Nadp+(A)) date Jul 18, 1994
title The Structure Of 6-Phosphogluconate Dehydrogenase Refined At Angstroms Resolution
authors M.J.Adams, C.Phillips, S.Gover
compound source
Molecule: 6-Phosphogluconate Dehydrogenase
Chain: A
Ec: 1.1.1.44
Engineered: Yes
 Organism_scientific: Ovis Aries
Organism_common: Sheep
Organism_taxid: 9940
symmetry Space Group: C 2 2 21
R_factor 0.198 R_Free NULL
crystal
cell
length a length b length c angle alpha angle beta angle gamma
72.740 148.400 102.350 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.00 Å
ligand SO4 enzyme Oxidoreductase E.C.1.1.1.44 BRENDA
note 2PGD supersedes 1PGD
related structures by homologous chain: 1PGN
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceThe structure of 6-phosphogluconate dehydrogenase refined at 2.5 A resolution., Adams MJ, Gover S, Leaback R, Phillips C, Somers DO, Acta Crystallogr B 1991 Oct 1;47 ( Pt 5):817-20. PMID:1793548
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (84 Kb) [Save to disk]
  • Biological Unit Coordinates (2pgd.pdb1.gz) 158 Kb
  • LPC: Ligand-Protein Contacts for 2PGD
  • CSU: Contacts of Structural Units for 2PGD
  • Likely Quarternary Molecular Structure file(s) for 2PGD
  • Structure Factors (337 Kb)
  • Retrieve 2PGD in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2PGD from S2C, [Save to disk]
  • Re-refined 2pgd structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 2PGD 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 2PGD
  • 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
  • 3D motif for 2PGD, from MSDmotif at EBI
  • Genome occurence of 2PGD's fold from GeneCensus
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d2pgd_2, region 1-176 [Jmol] [rasmolscript] [script source]
        - Domain d2pgd_1, region 177-473 [Jmol] [rasmolscript] [script source]
  • Class (fold), Architecture (subfold), Topology, Homologous superfamily from CATH
  • Summaries and structural analyses of PDB data files from PDBSum
  • Identification of Protein Pockets & Cavities at CASTp
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2pgd_A] [2pgd]
  • SWISS-PROT database: [P00349]
  • Domain organization of [6PGD_SHEEP] by SWISSPFAM
  • Domain found in 2PGD: [6PGD ] by SMART
    • Other resources with information on 2PGD
  • Community annotation for 2PGD at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
    • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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