4MDH Oxidoreductase(Nad(A)-Choh(D)) date Apr 12, 1989
title Refined Crystal Structure Of Cytoplasmic Malate Dehydrogenas Angstroms Resolution
authors J.J.Birktoft, L.J.Banaszak
compound source
Molecule: Cytoplasmic Malate Dehydrogenase
Chain: A, B
Ec: 1.1.1.37
Engineered: Yes
Organism_scientific: Sus Scrofa
Organism_common: Pig
Organism_taxid: 9823
symmetry Space Group: P 21 21 2
R_factor
R_Free NULL
crystal
cell
length a length b length c angle alpha angle beta angle gamma
139.200 86.600 58.800 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.50 Å
ligand ACE, NAD, SO4 enzyme Oxidoreductase E.C.1.1.1.37 BRENDA
note 4MDH supersedes 2MDH, 1MDH
related structures by homologous chain: 5MDH
Gene
Ontology
ChainFunctionProcessComponent
A, B


Primary referenceRefined crystal structure of cytoplasmic malate dehydrogenase at 2.5-A resolution., Birktoft JJ, Rhodes G, Banaszak LJ, Biochemistry 1989 Jul 11;28(14):6065-81. PMID:2775751
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (122 Kb) [Save to disk]
  • Biological Unit Coordinates (4mdh.pdb1.gz) 116 Kb
  • LPC: Ligand-Protein Contacts for 4MDH
  • CSU: Contacts of Structural Units for 4MDH
  • Likely Quarternary Molecular Structure file(s) for 4MDH
  • Structure Factors (125 Kb)
  • Retrieve 4MDH in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4MDH from S2C, [Save to disk]
  • Re-refined 4mdh structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4MDH 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 4MDH
  • 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 4MDH, from MSDmotif at EBI
  • Genome occurence of 4MDH's fold from GeneCensus
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d4mdha1, region A:1-154 [Jmol] [rasmolscript] [script source]
        - Domain d4mdha2, region A:155-333 [Jmol] [rasmolscript] [script source]
        - Domain d4mdhb1, region B:1-154 [Jmol] [rasmolscript] [script source]
        - Domain d4mdhb2, region B:155-333 [Jmol] [rasmolscript] [script source]
  • Fold representative 4mdh from FSSP and Dali (Families of Structurally Similar Proteins)
  • 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: [4mdh] [4mdh_A] [4mdh_B]
  • SWISS-PROT database: [P11708]
  • Domain organization of [MDHC_PIG] by SWISSPFAM
  • Other resources with information on 4MDH
  • Community annotation for 4MDH at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Domain movements in 4MDH from the Database of Macromolecular Movements.
  • Images from IMB Jena Image Library of Biological Macromolecules.

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