1GDH Oxidoreductase(Choh (D)-Nad(P)+ (A)) date Sep 22, 1993
title Crystal Structure Of A Nad-Dependent D-Glycerate Dehydrogena Angstroms Resolution
authors J.D.Goldberg, T.Yoshida, P.Brick
compound source
Molecule: D-Glycerate Dehydrogenase
Chain: A, B
Ec: 1.1.1.29
Engineered: Yes
Organism_scientific: Hyphomicrobium Methylovorum
Organism_taxid: 84
symmetry Space Group: P 1
R_factor 0.189 R_Free NULL
crystal
cell
length a length b length c angle alpha angle beta angle gamma
60.410 60.530 66.290 102.30 113.73 102.73
method X-Ray Diffractionresolution 2.40 Å
ligand SO4 enzyme Oxidoreductase E.C.1.1.1.29 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, B


Primary referenceCrystal structure of a NAD-dependent D-glycerate dehydrogenase at 2.4 A resolution., Goldberg JD, Yoshida T, Brick P, J Mol Biol 1994 Mar 4;236(4):1123-40. PMID:8120891
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (104 Kb) [Save to disk]
  • Biological Unit Coordinates (1gdh.pdb1.gz) 100 Kb
  • LPC: Ligand-Protein Contacts for 1GDH
  • CSU: Contacts of Structural Units for 1GDH
  • Likely Quarternary Molecular Structure file(s) for 1GDH
  • Structure Factors (198 Kb)
  • Retrieve 1GDH in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1GDH from S2C, [Save to disk]
  • Re-refined 1gdh structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1GDH 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 1GDH
  • 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 1GDH, from MSDmotif at EBI
  • Genome occurence of 1GDH's fold from GeneCensus
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1gdha1, region A:101-291 [Jmol] [rasmolscript] [script source]
        - Domain d1gdha2, region A:2-100,A:292-321 [Jmol] [rasmolscript] [script source]
        - Domain d1gdhb1, region B:101-291 [Jmol] [rasmolscript] [script source]
        - Domain d1gdhb2, region B:2-100,B:292-321 [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: [1gdh_B] [1gdh_A] [1gdh]
  • SWISS-PROT database: [P36234]
  • Domain organization of [DHGY_HYPME] by SWISSPFAM
  • Other resources with information on 1GDH
  • Community annotation for 1GDH at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Domain movements in 1GDH from the Database of Macromolecular Movements.
  • Images from IMB Jena Image Library of Biological Macromolecules.

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