1N1E Oxidoreductase date Oct 17, 2002
title Crystal Structure Of Leishmania Mexicana Glycerol-3-Phosphat Dehydrogenase Complexed With Dhap And Nad
authors J.Choe, W.G.J.Hol
compound source
Molecule: Glycerol-3-Phosphate Dehydrogenase
Chain: A, B
Ec: 1.1.1.8
Engineered: Yes
Organism_scientific: Leishmania Mexicana
Organism_taxid: 5665
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet3a
symmetry Space Group: P 65
R_factor 0.173 R_Free 0.195
crystal
cell
length a length b length c angle alpha angle beta angle gamma
77.745 77.745 266.631 90.00 90.00 120.00
method X-Ray Diffractionresolution 1.90 Å
ligand NDE enzyme Oxidoreductase E.C.1.1.1.8 BRENDA
related structures by homologous chain: 1EVY, 1M66
Gene
Ontology
ChainFunctionProcessComponent
A, B


Primary referenceLeishmania mexicana glycerol-3-phosphate dehydrogenase showed conformational changes upon binding a bi-substrate adduct., Choe J, Guerra D, Michels PA, Hol WG, J Mol Biol 2003 May 30;329(2):335-49. PMID:12758080
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (117 Kb) [Save to disk]
  • Biological Unit Coordinates (1n1e.pdb1.gz) 111 Kb
  • LPC: Ligand-Protein Contacts for 1N1E
  • CSU: Contacts of Structural Units for 1N1E
  • Likely Quarternary Molecular Structure file(s) for 1N1E
  • Structure Factors (563 Kb)
  • Retrieve 1N1E in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1N1E from S2C, [Save to disk]
  • Re-refined 1n1e structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1N1E 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 1N1E
  • 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
  • 3D motif for 1N1E, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1n1ea1, region A:198-357 [Jmol] [rasmolscript] [script source]
        - Domain d1n1ea2, region A:9-197 [Jmol] [rasmolscript] [script source]
        - Domain d1n1eb1, region B:198-357 [Jmol] [rasmolscript] [script source]
        - Domain d1n1eb2, region B:9-197 [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: [1n1e_B] [1n1e] [1n1e_A]
  • SWISS-PROT database: [P90551]
  • Domain organization of [GPDA_LEIME] by SWISSPFAM
  • Other resources with information on 1N1E
  • Community annotation for 1N1E 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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