2DXU Ligase date Aug 30, 2006
title Crystal Structure Of Biotin Protein Ligase From Pyrococcus H Complexed With Biotinyl-5'-Amp, Mutation R48a
authors B.Bagautdinov, M.Taketa, Y.Matsuura, N.Kunishima, Riken Structur Genomicsproteomics Initiative (Rsgi)
compound source
Molecule: Biotin--[Acetyl-Coa-Carboxylase] Ligase
Chain: A, B
Synonym: Biotin Protein Ligase
Ec: 6.3.4.15
Engineered: Yes
Mutation: Yes
Organism_scientific: Pyrococcus Horikoshii
Organism_taxid: 53953
Gene: Bira
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: (De3)Ril
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet 11a
symmetry Space Group: P 1 21 1
R_factor 0.223 R_Free 0.233
crystal
cell
length a length b length c angle alpha angle beta angle gamma
38.236 82.851 72.354 90.00 101.37 90.00
method X-Ray Diffractionresolution 1.28 Å
ligand BT5 enzyme Ligase E.C.6.3.4.15 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, B


Primary referenceProtein biotinylation visualized by a complex structure of biotin protein ligase with a substrate., Bagautdinov B, Matsuura Y, Bagautdinova S, Kunishima N, J Biol Chem. 2008 May 23;283(21):14739-50. Epub 2008 Mar 26. PMID:18372281
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (86 Kb) [Save to disk]
  • Biological Unit Coordinates (2dxu.pdb1.gz) 82 Kb
  • LPC: Ligand-Protein Contacts for 2DXU
  • CSU: Contacts of Structural Units for 2DXU
  • Likely Quarternary Molecular Structure file(s) for 2DXU
  • Structure Factors (848 Kb)
  • Retrieve 2DXU in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2DXU from S2C, [Save to disk]
  • Re-refined 2dxu structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2DXU 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 2DXU
  • 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 2DXU, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2dxu_A] [2dxu] [2dxu_B]
  • SWISS-PROT database: [O57883]
  • Domain organization of [O57883_PYRHO] by SWISSPFAM
  • Other resources with information on 2DXU
  • Community annotation for 2DXU 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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