3DYI Hydrolase date Jul 28, 2008
title Snapshots Of Esterase D From Lactobacillus Rhamnosus: Insights Into A Rotation Driven Catalytic Mechanism
authors M.D.Bennett, M.L.Delabre, R.Holland, G.E.Norris
compound source
Molecule: Esterase D
Chain: A
Engineered: Yes
 Organism_scientific: Lactobacillus Rhamnosus
Organism_taxid: 486408
Strain: Hn001
Gene: Estd
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pproexht C
symmetry Space Group: P 32 2 1
R_factor 0.177 R_Free 0.201
crystal
cell
length a length b length c angle alpha angle beta angle gamma
47.442 47.442 174.180 90.00 90.00 120.00
method X-Ray Diffractionresolution 1.72 Å
ligand CL enzyme
Gene
Ontology
ChainFunctionProcessComponent
A


Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (46 Kb) [Save to disk]
  • Biological Unit Coordinates (3dyi.pdb1.gz) 42 Kb
  • LPC: Ligand-Protein Contacts for 3DYI
  • CSU: Contacts of Structural Units for 3DYI
  • Likely Quarternary Molecular Structure file(s) for 3DYI
  • Structure Factors (339 Kb)
  • Retrieve 3DYI in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3DYI from S2C, [Save to disk]
  • Re-refined 3dyi structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 3DYI 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 3DYI
  • 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 3DYI, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3dyi_A] [3dyi]
  • SWISS-PROT database: [B2CZF3]
  • Domain organization of [B2CZF3_LACRH] by SWISSPFAM
    • Other resources with information on 3DYI
  • Community annotation for 3DYI at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
    • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

    • 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