5MDH Oxidoreductase date Oct 08, 1998
title Crystal Structure Of Ternary Complex Of Porcine Cytoplasmic Dehydrogenase Alpha-Ketomalonate And Tnad At 2.4 Angstroms
authors A.D.M.Chapman, A.Cortes, T.R.Dafforn, A.R.Clarke, R.L.Brady
compound source
Molecule: Malate Dehydrogenase
Chain: A, B
Engineered: Yes
Organism_scientific: Sus Scrofa
Organism_common: Pig
Organism_taxid: 9823
Organ: Heart
Tissue: Muscle
Cellular_location: Cytoplasm
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: P 21 21 2
R_factor 0.199 R_Free 0.253
length a length b length c angle alpha angle beta angle gamma
85.700 144.432 59.226 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.40 Å
ligand MAK, NAD enzyme Oxidoreductase E.C. BRENDA
note 5MDH (Molecule of the Month:pdb154)
related structures by homologous chain: 4MDH
A, B

Primary referenceStructural basis of substrate specificity in malate dehydrogenases: crystal structure of a ternary complex of porcine cytoplasmic malate dehydrogenase, alpha-ketomalonate and tetrahydoNAD., Chapman AD, Cortes A, Dafforn TR, Clarke AR, Brady RL, J Mol Biol 1999 Jan 15;285(2):703-12. PMID:10075524
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (117 Kb) [Save to disk]
  • Biological Unit Coordinates (5mdh.pdb1.gz) 111 Kb
  • LPC: Ligand-Protein Contacts for 5MDH
  • CSU: Contacts of Structural Units for 5MDH
  • Likely Quarternary Molecular Structure file(s) for 5MDH
  • Retrieve 5MDH in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5MDH from S2C, [Save to disk]
  • View 5MDH 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 5MDH
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 5MDH, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d5mdha1, region A:1-154 [Jmol] [rasmolscript] [script source]
        - Domain d5mdha2, region A:155-333 [Jmol] [rasmolscript] [script source]
        - Domain d5mdhb1, region B:1-154 [Jmol] [rasmolscript] [script source]
        - Domain d5mdhb2, region B:155-333 [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: [5mdh] [5mdh_B] [5mdh_A]
  • SWISS-PROT database: [P11708]
  • Domain organization of [MDHC_PIG] by SWISSPFAM
  • Other resources with information on 5MDH
  • Community annotation for 5MDH 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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