2P88 Lyase date Mar 22, 2007
title Crystal Structure Of N-Succinyl Arglys Racemase From Bacill Atcc 14579
authors A.A.Fedorov, L.Song, E.V.Fedorov, J.A.Gerlt, S.C.Almo
compound source
Molecule: Mandelate Racemasemuconate Lactonizing Enzyme Fa Protein;
Chain: A, B, C, D, E, F, G, H
Engineered: Yes
 Organism_scientific: Bacillus Cereus Atcc 14579
Organism_taxid: 226900
Strain: Dsm 31
Gene: Bc_0371
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: P 1 21 1
R_factor 0.221 R_Free 0.239
crystal
cell
length a length b length c angle alpha angle beta angle gamma
135.953 94.610 135.956 90.00 90.16 90.00
method X-Ray Diffractionresolution 2.40 Å
ligand MG enzyme
Gene BC
Gene
Ontology
ChainFunctionProcessComponent
F, A, E, B, H, C, D, G


Primary referencePrediction and assignment of function for a divergent N-succinyl amino acid racemase., Song L, Kalyanaraman C, Fedorov AA, Fedorov EV, Glasner ME, Brown S, Imker HJ, Babbitt PC, Almo SC, Jacobson MP, Gerlt JA, Nat Chem Biol. 2007 Aug;3(8):486-91. Epub 2007 Jul 1. PMID:17603539
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (463 Kb) [Save to disk]
  • Biological Unit Coordinates (2p88.pdb1.gz) 458 Kb
  • LPC: Ligand-Protein Contacts for 2P88
  • CSU: Contacts of Structural Units for 2P88
  • Likely Quarternary Molecular Structure file(s) for 2P88
  • Structure Factors (1646 Kb)
  • Retrieve 2P88 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2P88 from S2C, [Save to disk]
  • Re-refined 2p88 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 2P88 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 2P88
  • 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 2P88, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2p88] [2p88_A] [2p88_C] [2p88_G] [2p88_E] [2p88_D] [2p88_H] [2p88_B] [2p88_F]
  • SWISS-PROT database: [Q81IL5]
  • Domain organization of [Q81IL5_BACCR] by SWISSPFAM
  • Domain found in 2P88: [MR_MLE ] by SMART
    • Other resources with information on 2P88
  • Community annotation for 2P88 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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