2OKL Hydrolase date Jan 17, 2007
title Crystal Structure Of Peptide Deformylase 2 With Actinonin Fr Bacillus Cereus
authors E.E.Kim
compound source
Molecule: Peptide Deformylase 2
Chain: A, B
Synonym: Pdf 2, Polypeptide Deformylase 2
Ec: 3.5.1.88
Engineered: Yes
Organism_scientific: Bacillus Cereus
Organism_taxid: 226900
Strain: Atcc 14579
Gene: Def2
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21 (De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet28a
symmetry Space Group: P 65 2 2
R_factor 0.228 R_Free 0.257
crystal
cell
length a length b length c angle alpha angle beta angle gamma
69.447 69.447 294.412 90.00 90.00 120.00
method X-Ray Diffractionresolution 1.70 Å
ligand BB2, CIT, ZN enzyme Hydrolase E.C.3.5.1.88 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, B


Primary referenceCharacterization of peptide deformylase2 from B. cereus., Park JK, Kim KH, Moon JH, Kim EE, J Biochem Mol Biol. 2007 Nov 30;40(6):1050-7. PMID:18047803
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (73 Kb) [Save to disk]
  • Biological Unit Coordinates (2okl.pdb1.gz) 35 Kb
  • Biological Unit Coordinates (2okl.pdb2.gz) 35 Kb
  • LPC: Ligand-Protein Contacts for 2OKL
  • CSU: Contacts of Structural Units for 2OKL
  • Likely Quarternary Molecular Structure file(s) for 2OKL
  • Retrieve 2OKL in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2OKL from S2C, [Save to disk]
  • View 2OKL 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 2OKL
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 2OKL, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2okl_B] [2okl_A] [2okl]
  • SWISS-PROT database: [Q819K2]
  • Domain organization of [DEF2_BACCR] by SWISSPFAM
  • Other resources with information on 2OKL
  • Community annotation for 2OKL 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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