1YGE Dioxygenase date Jun 04, 1996
title Lipoxygenase-1 (Soybean) At 100k
authors W.Minor, J.Steczko, B.Stec, Z.Otwinowski, J.T.Bolin, R.Walter, B.A
compound source
Molecule: Lipoxygenase-1
Chain: A
Synonym: L-1
Ec: 1.13.11.12
 Organism_scientific: Glycine Max
Organism_common: Soybean
Organism_taxid: 3847
symmetry Space Group: P 1 21 1
R_factor 0.197 R_Free 0.243
crystal
cell
length a length b length c angle alpha angle beta angle gamma
94.900 94.000 49.900 90.00 90.10 90.00
method X-Ray Diffractionresolution 1.40 Å
ligand FE enzyme Oxidoreductase E.C.1.13.11.12 BRENDA
related structures by homologous chain: 1F8N
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceCrystal structure of soybean lipoxygenase L-1 at 1.4 A resolution., Minor W, Steczko J, Stec B, Otwinowski Z, Bolin JT, Walter R, Axelrod B, Biochemistry 1996 Aug 20;35(33):10687-701. PMID:8718858
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (165 Kb) [Save to disk]
  • Biological Unit Coordinates (1yge.pdb1.gz) 161 Kb
  • LPC: Ligand-Protein Contacts for 1YGE
  • CSU: Contacts of Structural Units for 1YGE
  • Likely Quarternary Molecular Structure file(s) for 1YGE
  • Retrieve 1YGE in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1YGE from S2C, [Save to disk]
    • View 1YGE 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 1YGE
  • Ramachandran plot from PDBSum
    • Structure-derived information
  • Conformational Epitope Prediction for 1YGE from the CEP Server.
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 1YGE, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1yge_2, region 1-149 [Jmol] [rasmolscript] [script source]
        - Domain d1yge_1, region 150-839 [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: [1yge] [1yge_A]
  • SWISS-PROT database: [P08170]
  • Domain organization of [LOX1_SOYBN] by SWISSPFAM
  • Domain found in 1YGE: [LH2 ] by SMART
    • Other resources with information on 1YGE
  • Community annotation for 1YGE 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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