3JD4 Oxidoreductase date Mar 28, 2016
title Glutamate Dehydrogenase In Complex With Nadh And Gtp, Closed Conformation
authors M.J.Borgnia, S.Banerjee, A.Merk, D.Matthies, A.Bartesaghi, P.Rao, J.Pierson, L.A.Earl, V.Falconieri, S.Subramaniam, J.L.S.Milne
compound source
Molecule: Glutamate Dehydrogenase 1, Mitochondrial
Chain: A, B, C, D, E, F
Fragment: Unp Residues 58-558
Synonym: Gdh 1
Ec: 1.4.1.3
 Organism_scientific: Bos Taurus
Organism_common: Bovine
Organism_taxid: 9913
symmetry Space Group: P 1
R_factor
R_Free
crystal
cell
length a length b length c angle alpha angle beta angle gamma
1.000 1.000 1.000 90.00 90.00 90.00
method Electron Microscopyresolution 3.40 Å
ligand GTP, NAI enzyme Oxidoreductase E.C.1.4.1.3 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
F, A, D, C, E, B


Primary referenceUsing Cryo-EM to Map Small Ligands on Dynamic Metabolic Enzymes: Studies with Glutamate Dehydrogenase., Borgnia MJ, Banerjee S, Merk A, Matthies D, Bartesaghi A, Rao P, Pierson J, Earl LA, Falconieri V, Subramaniam S, Milne JL, Mol Pharmacol. 2016 Jun;89(6):645-51. doi: 10.1124/mol.116.103382. Epub 2016 Apr , 1. PMID:27036132
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (473 Kb) [Save to disk]
  • Biological Unit Coordinates (3jd4.pdb1.gz) 464 Kb
  • LPC: Ligand-Protein Contacts for 3JD4
  • CSU: Contacts of Structural Units for 3JD4
  • Retrieve 3JD4 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3JD4 from S2C, [Save to disk]
    • View 3JD4 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 3JD4
  • Ramachandran plot from PDBSum
    • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3jd4_D] [3jd4_E] [3jd4_F] [3jd4_A] [3jd4] [3jd4_C] [3jd4_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 3JD4: [ELFV_dehydrog ] by SMART
    • Other resources with information on 3JD4
  • Community annotation for 3JD4 at PDBWiki (http://pdbwiki.org)

    • You may enter another PDB ID code
    Go [Back], to the [PDB Lite page], to the [OCA Search page] or to the [PDB Home page]
    OCA© by Jaime Prilusky, 1996-2014,2022
    Bioinformatics Unit
    Weizmann Institute of Science