2OTY Hydrolase date Feb 09, 2007
title 1,2-Dichlorobenzene In Complex With T4 Lysozyme L99a
authors A.P.Graves, B.K.Shoichet
compound source
Molecule: Lysozyme
Chain: X
Synonym: Lysis Protein, Muramidase, Endolysin
Ec: 3.2.1.17
Engineered: Yes
Organism_scientific: Enterobacteria Phage T4
Organism_taxid: 10665
Gene: E
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_vector_type: Plasmid
Expression_system_plasmid: M13
symmetry Space Group: P 32 2 1
R_factor 0.196 R_Free 0.235
crystal
cell
length a length b length c angle alpha angle beta angle gamma
60.210 60.210 97.031 90.00 90.00 120.00
method X-Ray Diffractionresolution 1.83 Å
ligand BME, PO4, YAN enzyme Hydrolase E.C.3.2.1.17 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
X


Primary referencePredicting absolute ligand binding free energies to a simple model site., Mobley DL, Graves AP, Chodera JD, McReynolds AC, Shoichet BK, Dill KA, J Mol Biol. 2007 Aug 24;371(4):1118-34. Epub 2007 Jun 8. PMID:17599350
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (36 Kb) [Save to disk]
  • Biological Unit Coordinates (2oty.pdb1.gz) 32 Kb
  • LPC: Ligand-Protein Contacts for 2OTY
  • CSU: Contacts of Structural Units for 2OTY
  • Likely Quarternary Molecular Structure file(s) for 2OTY
  • Structure Factors (166 Kb)
  • Retrieve 2OTY in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2OTY from S2C, [Save to disk]
  • Re-refined 2oty structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2OTY 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 2OTY
  • 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 2OTY, from MSDmotif at EBI
  • Fold representative 2oty from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2oty_X] [2oty]
  • SWISS-PROT database: [P00720]
  • Domain organization of [LYS_BPT4] by SWISSPFAM
  • Other resources with information on 2OTY
  • Community annotation for 2OTY 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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