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 Diffraction	resolution	2.27 Å
ligand	VO4	enzyme	Isomerase E.C.5.99.1.2 BRENDA
note	2B9S is a representative structure
Gene Ontology	Chain Function Process Component A B
Primary reference	The 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] (99 Kb) [Save to disk] Biological Unit Coordinates (2b9s.pdb1.gz) 93 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

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 2B9S, from MSDmotif at EBI

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)

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