2B9S Isomerase Dna date Oct 12, 2005
title Crystal Structure Of Heterodimeric L. Donovani Topoisomerase Vanadate-Dna Complex
authors D.R.Davies, W.G.J.Hol
compound source
Molecule: 5'-D(Apapapapapgpapcptpt)-3'
Chain: C
Engineered: Yes
Synthetic: Yes

Molecule: 5'-D(Apgpapapapapaptptptptpt)-3'
Chain: D
Engineered: Yes

Synthetic: Yes

Molecule: 5'-D(Apapapapaptptptptptpcptpapapg Tptptpt)-3';
Chain: E
Engineered: Yes

Synthetic: Yes

Molecule: Topoisomerase I-Like Protein
Chain: A
Ec: 5.99.1.2
Engineered: Yes

Organism_scientific: Leishmania Donovani
Organism_taxid: 5661
Gene: Topoisomerase I, Large Subunit (Ldtop1l)
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21 (De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Plyss

Molecule: Dna Topoisomerase I-Like Protein
Chain: B
Ec: 5.99.1.2
Engineered: Yes

Organism_scientific: Leishmania Donovani
Organism_taxid: 5661
Gene: Topoisomerase I, Small Subunit (Ldtop1s)
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21 (De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Plyss
symmetry Space Group: P 21 21 21
R_factor 0.231 R_Free 0.275
crystal
cell
length a length b length c angle alpha angle beta angle gamma
72.433 106.102 126.691 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.27 Å
ligand VO4 enzyme Isomerase E.C.5.99.1.2 BRENDA
note 2B9S is a representative structure
Gene
Ontology
ChainFunctionProcessComponent
A


B


Primary referenceThe structure of the transition state of the heterodimeric topoisomerase I of Leishmania donovani as a vanadate complex with nicked DNA., Davies DR, Mushtaq A, Interthal H, Champoux JJ, Hol WG, J Mol Biol. 2006 Apr 7;357(4):1202-10. Epub 2006 Jan 26. PMID:16487540
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (101 Kb) [Save to disk]
  • Biological Unit Coordinates (2b9s.pdb1.gz) 95 Kb
  • LPC: Ligand-Protein Contacts for 2B9S
  • CSU: Contacts of Structural Units for 2B9S
  • Likely Quarternary Molecular Structure file(s) for 2B9S
  • Structure Factors (601 Kb)
  • Retrieve 2B9S in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2B9S from S2C, [Save to disk]
  • Re-refined 2b9s structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2B9S 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 2B9S
  • 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 2B9S, from MSDmotif at EBI
  • Fold representative 2b9s from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2b9s] [2b9s_A] [2b9s_C] [2b9s_B] [2b9s_D] [2b9s_E]
  • SWISS-PROT database: [Q8WQM6] [Q9GPZ9]
  • Domain organization of [Q8WQM6_LEIDO] [Q9GPZ9_LEIIN] by SWISSPFAM
  • Domain found in 2B9S: [TOPEUc ] by SMART
  • Other resources with information on 2B9S
  • Community annotation for 2B9S 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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