5JD3 Hydrolase date Apr 15, 2016
title Crystal Structure Of Lae5, An Alphabeta Hydrolase Enzyme Fr Metagenome Of Lake Arreo, Spain
authors P.J.Stogios, X.Xu, B.Nocek, H.Cui, V.Yim, M.Martinez-Martinez, M.A M.Ferrer, A.Savchenko
compound source
Molecule: Lae5
Chain: A, B, C, D, E, F, G, H
Engineered: Yes
 Organism_scientific: Uncultured Bacterium
Organism_taxid: 77133
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: P15tv Lic
symmetry Space Group: P 1 21 1
R_factor 0.184 R_Free 0.236
crystal
cell
length a length b length c angle alpha angle beta angle gamma
66.591 129.452 129.848 90.00 97.49 90.00
method X-Ray Diffractionresolution 2.30 Å
ligand CL, PEG, SO4 enzyme
Gene
Ontology
ChainFunctionProcessComponent
F, A, E, B, H, C, D, G


Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (598 Kb) [Save to disk]
  • Biological Unit Coordinates (5jd3.pdb1.gz) 76 Kb
  • Biological Unit Coordinates (5jd3.pdb2.gz) 77 Kb
  • Biological Unit Coordinates (5jd3.pdb3.gz) 77 Kb
  • Biological Unit Coordinates (5jd3.pdb4.gz) 77 Kb
  • Biological Unit Coordinates (5jd3.pdb5.gz) 77 Kb
  • Biological Unit Coordinates (5jd3.pdb6.gz) 76 Kb
  • Biological Unit Coordinates (5jd3.pdb7.gz) 76 Kb
  • Biological Unit Coordinates (5jd3.pdb8.gz) 77 Kb
  • Biological Unit Coordinates (5jd3.pdb9.gz) 149 Kb
  • LPC: Ligand-Protein Contacts for 5JD3
  • CSU: Contacts of Structural Units for 5JD3
  • Structure Factors (1058 Kb)
  • Retrieve 5JD3 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5JD3 from S2C, [Save to disk]
  • Re-refined 5jd3 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 5JD3 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 5JD3
  • 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
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5jd3] [5jd3_F] [5jd3_A] [5jd3_G] [5jd3_C] [5jd3_H] [5jd3_D] [5jd3_B] [5jd3_E]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 5JD3
  • Community annotation for 5JD3 at PDBWiki (http://pdbwiki.org)

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