5BS3	Isomerase Dna Rna	date	Jun 01, 2015
title	Crystal Structure Of S.A. Gyrase In Complex With Compound 7
authors	J.Lu, S.Patel, S.Soisson
compound		source
Molecule: Dna Gyrase Subunit A And B Chain: B, D Ec: 5.99.1.3 Engineered: Yes		Organism_scientific: Staphylococcus Aureus Organism_taxid: 1280 Gene: Gyrb, Gyra Expression_system: Escherichia Coli Expression_system_taxid: 562
Molecule: Dnarna (5'-R(Papgpcpcpg)-D(Pt)- R(Papgpgpgpcpcpc)-D(Pt)-R(Papcpgpgpc)-D(Pt)-3 Chain: E, F Engineered: Yes		Synthetic: Yes Organism_scientific: Staphylococcus Aureus Subsp. Aureus Ed Organism_taxid: 681288
symmetry	Space Group: P 61	R_factor 0.170 R_Free 0.213
crystal cell	length a length b length c angle alpha angle beta angle gamma 93.337 93.337 411.068 90.00 90.00 120.00
method	X-Ray Diffraction	resolution	2.65 Å
ligand	MN, SO4, WCP	enzyme	Isomerase E.C.5.99.1.3 BRENDA
Gene Ontology	Chain Function Process Component D, B
Primary reference	Tricyclic 1,5-naphthyridinone oxabicyclooctane-linked novel bacterial topoisomerase inhibitors as broad-spectrum antibacterial agents-SAR of left-hand-side moiety (Part-2)., Singh SB, Kaelin DE, Wu J, Miesel L, Tan CM, Black T, Nargund R, Meinke PT, Olsen DB, Lagrutta A, Lu J, Patel S, Rickert KW, Smith RF, Soisson S, Sherer E, Joyce LA, Wei C, Peng X, Wang X, Fukuda H, Kishii R, Takei M, Takano H, Shibasaki M, Yajima M, Nishimura A, Shibata T, Fukuda Y, Bioorg Med Chem Lett. 2015 May 1;25(9):1831-5. doi: 10.1016/j.bmcl.2015.03.044., Epub 2015 Mar 24. PMID:25851938

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (233 Kb) [Save to disk] Biological Unit Coordinates (5bs3.pdb1.gz) 226 Kb LPC: Ligand-Protein Contacts for 5BS3 CSU: Contacts of Structural Units for 5BS3 Structure Factors (1483 Kb) Retrieve 5BS3 in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 5BS3 from S2C, [Save to disk] Re-refined 5bs3 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 5BS3 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 5BS3

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 5BS3, from MSDmotif at EBI

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [5bs3_B] [5bs3] [5bs3_F] [5bs3_E] [5bs3_D] SWISS-PROT database: Domain organization of by SWISSPFAM Domains found in 5BS3: [TOP2c] [TOP4c ] by SMART

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