1ZMD Oxidoreductase date May 10, 2005
title Crystal Structure Of Human Dihydrolipoamide Dehydrogenase Complexed To Nadh
authors C.A.Brautigam, J.L.Chuang, D.R.Tomchick, M.Machius, D.T.Chuang
compound source
Molecule: Dihydrolipoyl Dehydrogenase
Chain: A, B, C, D, E, F, G, H
Synonym: Dihydrolipoamide Dehydrogenase, Glycine Cleavage System L Protein;
Ec: 1.8.1.4
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Dld, Gcsl, Lad, Phe3
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Xl1-Blue
Expression_system_vector_type: Ptrchisthe3
Expression_system_plasmid: Plasmid
symmetry Space Group: P 21 21 2
R_factor 0.221 R_Free 0.249
crystal
cell
length a length b length c angle alpha angle beta angle gamma
175.871 210.914 127.096 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.08 Å
ligand FAD, NAI, SO4 enzyme Oxidoreductase E.C.1.8.1.4 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
F, A, E, B, H, C, D, G
  • pyruvate dehydrogenase (NAD+...


  • Primary referenceCrystal Structure of Human Dihydrolipoamide Dehydrogenase: NAD(+)/NADH Binding and the Structural Basis of Disease-causing Mutations., Brautigam CA, Chuang JL, Tomchick DR, Machius M, Chuang DT, J Mol Biol 2005 Jul 15;350(3):543-52. PMID:15946682
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (636 Kb) [Save to disk]
  • Biological Unit Coordinates (1zmd.pdb1.gz) 163 Kb
  • Biological Unit Coordinates (1zmd.pdb2.gz) 163 Kb
  • Biological Unit Coordinates (1zmd.pdb3.gz) 166 Kb
  • Biological Unit Coordinates (1zmd.pdb4.gz) 167 Kb
  • LPC: Ligand-Protein Contacts for 1ZMD
  • CSU: Contacts of Structural Units for 1ZMD
  • Likely Quarternary Molecular Structure file(s) for 1ZMD
  • Structure Factors (2441 Kb)
  • Retrieve 1ZMD in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1ZMD from S2C, [Save to disk]
  • Re-refined 1zmd structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1ZMD 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 1ZMD
  • 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 1ZMD, from MSDmotif at EBI
  • Fold representative 1zmd from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1zmd_B] [1zmd_A] [1zmd_E] [1zmd_D] [1zmd_C] [1zmd_H] [1zmd_F] [1zmd] [1zmd_G]
  • SWISS-PROT database: [P09622]
  • Domain organization of [DLDH_HUMAN] by SWISSPFAM
  • Other resources with information on 1ZMD
  • Community annotation for 1ZMD at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
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