2VLE Oxidoreductase date Jan 13, 2008
title The Structure Of Daidzin, A Naturally Occurring Anti Alcohol-Addiction Agent, In Complex With Human Mitochondrial Aldehyde Dehydrogenase
authors E.D.Lowe, G.Y.Gao, L.N.Johnson, W.M.Keung
compound source
Molecule: Aldehyde Dehydrogenase, Mitochondrial
Chain: A, B, C, D, E, F, G, H
Fragment: Residues 24-517
Synonym: Aldh Class 2, Aldhi, Aldh-E2
Ec: 1.2.1.3
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Organ: Liver
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_plasmid: Pt7-7
symmetry Space Group: P 21 21 21
R_factor 0.1962 R_Free 0.2495
crystal
cell
length a length b length c angle alpha angle beta angle gamma
142.770 150.990 176.990 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.4 Å
ligand DZN BindingDB enzyme Oxidoreductase E.C.1.2.1.3 BRENDA
note 2VLE supersedes 1OF7
Gene
Ontology
ChainFunctionProcessComponent
F, A, E, B, H, C, D, G


Primary referenceStructure of daidzin, a naturally occurring anti-alcohol-addiction agent, in complex with human mitochondrial aldehyde dehydrogenase., Lowe ED, Gao GY, Johnson LN, Keung WM, J Med Chem. 2008 Aug 14;51(15):4482-7. Epub 2008 Jul 10. PMID:18613661
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (1276 Kb) [Save to disk]
  • Biological Unit Coordinates (2vle.pdb1.gz) 640 Kb
  • Biological Unit Coordinates (2vle.pdb2.gz) 635 Kb
  • LPC: Ligand-Protein Contacts for 2VLE
  • CSU: Contacts of Structural Units for 2VLE
  • Likely Quarternary Molecular Structure file(s) for 2VLE
  • Structure Factors (1188 Kb)
  • Retrieve 2VLE in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2VLE from S2C, [Save to disk]
  • Re-refined 2vle structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2VLE 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 2VLE
  • 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 2VLE, from MSDmotif at EBI
  • Fold representative 2vle from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2vle] [2vle_H] [2vle_E] [2vle_B] [2vle_D] [2vle_F] [2vle_G] [2vle_A] [2vle_C]
  • SWISS-PROT database: [P05091]
  • Domain organization of [ALDH2_HUMAN] by SWISSPFAM
  • Alignments of the sequence of 2VLE with the sequences similar proteins can be viewed for 2VLE's classification [ALDH2_HUMAN] at ProtoMap. Click on "Neighbors List", then on the "See Alignments" button below the list.
  • A sequence distance tree ("phylogenetic tree") can be viewed for 1ACL's classification [ALDH2_HUMAN] at ProtoMap. Click on the Cluster number.
  • Other resources with information on 2VLE
  • Community annotation for 2VLE 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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