2DFD Oxidoreductase date Feb 28, 2006
title Crystal Structure Of Human Malate Dehydrogenase Type 2
authors E.Ugochukwu, N.Shafqat, A.Rojkova, M.Sundstrom, C.Arrowsmith, J.W A.Edwards, F.Von Delft, U.Oppermann, Structural Genomics Conso (Sgc)
compound source
Molecule: Malate Dehydrogenase
Chain: A, B, C, D
Synonym: Malate Dehydrogenase Type 2
Ec: 1.1.1.37
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Mdh2
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Rosetta
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pnic28-Bsa4
symmetry Space Group: P 21 21 21
R_factor 0.156 R_Free 0.194
crystal
cell
length a length b length c angle alpha angle beta angle gamma
59.943 152.526 154.827 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.90 Å
ligand ALA, CL, HIS, MLT, NAD enzyme Oxidoreductase E.C.1.1.1.37 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, D, C, B


Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (215 Kb) [Save to disk]
  • Biological Unit Coordinates (2dfd.pdb1.gz) 103 Kb
  • Biological Unit Coordinates (2dfd.pdb2.gz) 107 Kb
  • Biological Unit Coordinates (2dfd.pdb3.gz) 206 Kb
  • LPC: Ligand-Protein Contacts for 2DFD
  • CSU: Contacts of Structural Units for 2DFD
  • Likely Quarternary Molecular Structure file(s) for 2DFD
  • Structure Factors (1654 Kb)
  • Retrieve 2DFD in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2DFD from S2C, [Save to disk]
  • Re-refined 2dfd structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2DFD 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 2DFD
  • 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 2DFD, from MSDmotif at EBI
  • Fold representative 2dfd from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2dfd_C] [2dfd_B] [2dfd_D] [2dfd] [2dfd_A]
  • SWISS-PROT database: [P40926]
  • Domain organization of [MDHM_HUMAN] by SWISSPFAM
  • Other resources with information on 2DFD
  • Community annotation for 2DFD 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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