1BFD BENZOYLFORMATE DECARBOXYLASE FROM PSEUDOMONAS PUTIDA date
authors Hasson, M.S., Muscate, A., Mcleish, M.J., Polovnikova, L.S., Gerlt, J.A., Kenyon, G.L., Petsko, G.A., Ringe, D.
compound source
symmetry
R_factor
R_Free 0.1860000
crystal
cell
length a length b length c angle alpha angle beta angle gamma
method X-Ray Diffractionresolution 1.60
ligand CA, MG, TPP enzyme
related structures by homologous chain: 1MCZ, 1PI3
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceThe crystal structure of benzoylformate decarboxylase at 1.6 A resolution: diversity of catalytic residues in thiamin diphosphate-dependent enzymes., Hasson MS, Muscate A, McLeish MJ, Polovnikova LS, Gerlt JA, Kenyon GL, Petsko GA, Ringe D, Biochemistry 1998 Jul 14;37(28):9918-30. PMID:9665697
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (93 Kb) [Save to disk]
  • Biological Unit Coordinates (1bfd.pdb1.gz) 343 Kb
  • LPC: Ligand-Protein Contacts for 1BFD
  • CSU: Contacts of Structural Units for 1BFD
  • Likely Quarternary Molecular Structure file(s) for 1BFD
  • Structure Factors (462 Kb)
  • Retrieve 1BFD in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1BFD from S2C, [Save to disk]
  • Re-refined 1bfd structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 1BFD 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 1BFD
  • 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 1BFD, from MSDmotif at EBI
  • Genome occurence of 1BFD's fold from GeneCensus
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1bfd_1, region 182-341 [Jmol] [rasmolscript] [script source]
        - Domain d1bfd_2, region 2-181 [Jmol] [rasmolscript] [script source]
        - Domain d1bfd_3, region 342-524 [Jmol] [rasmolscript] [script source]
  • Class (fold), Architecture (subfold), Topology, Homologous superfamily from CATH
  • Summaries and structural analyses of PDB data files from PDBSum
  • Identification of Protein Pockets & Cavities at CASTp
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1bfd_A] [1bfd]
  • SWISS-PROT database: [P20906]
  • Domain organization of [MDLC_PSEPU] by SWISSPFAM
    • Other resources with information on 1BFD
  • Community annotation for 1BFD 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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