1BDM Oxidoreductase(Nad(A)-Choh(D)) date Feb 16, 1993
title The Structure At 1.8 Angstroms Resolution Of A Single Site M (T189i) Of Malate Dehydrogenase From Thermus Flavus With In Enzymatic Activity
authors C.A.Kelly, J.J.Birktoft
compound source
Molecule: Malate Dehydrogenase
Chain: A, B
Ec: 1.1.1.37
Engineered: Yes
 Organism_scientific: Thermus Thermophilus
Organism_taxid: 274
Expression_system_vector_type: Bacterium
symmetry Space Group: P 21 21 21
R_factor 0.169 R_Free NULL
crystal
cell
length a length b length c angle alpha angle beta angle gamma
71.750 88.640 118.970 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.80 Å
ligand NAX enzyme Oxidoreductase E.C.1.1.1.37 BRENDA
related structures by homologous chain: 1BMD
Gene
Ontology
ChainFunctionProcessComponent
A, B


Primary referenceDeterminants of protein thermostability observed in the 1.9-A crystal structure of malate dehydrogenase from the thermophilic bacterium Thermus flavus., Kelly CA, Nishiyama M, Ohnishi Y, Beppu T, Birktoft JJ, Biochemistry. 1993 Apr 20;32(15):3913-22. PMID:8471603
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (109 Kb) [Save to disk]
  • Biological Unit Coordinates (1bdm.pdb1.gz) 104 Kb
  • LPC: Ligand-Protein Contacts for 1BDM
  • CSU: Contacts of Structural Units for 1BDM
  • Likely Quarternary Molecular Structure file(s) for 1BDM
  • Retrieve 1BDM in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1BDM from S2C, [Save to disk]
    • View 1BDM 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 1BDM
  • Ramachandran plot from PDBSum
    • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 1BDM, from MSDmotif at EBI
  • Genome occurence of 1BDM's fold from GeneCensus
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1bdma1, region A:0-154 [Jmol] [rasmolscript] [script source]
        - Domain d1bdma2, region A:155-332 [Jmol] [rasmolscript] [script source]
        - Domain d1bdmb1, region B:0-154 [Jmol] [rasmolscript] [script source]
        - Domain d1bdmb2, region B:155-332 [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: [1bdm_A] [1bdm_B] [1bdm]
  • SWISS-PROT database: [P10584]
  • Domain organization of [MDH_THETH] by SWISSPFAM
    • Other resources with information on 1BDM
  • Community annotation for 1BDM 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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