6WAA Isomerase Dna Isomerase Inhibitor date Mar 24, 2020
title K. Pneumoniae Topoisomerase Iv (Pare-Parc) In Complex With D Compound 34 (7-[(1s,5r)-1-Amino-3-Azabicyclo[3.1.0]Hexan-3- (Aminomethyl)-1-Cyclopropyl-3,6-Difluoro-8-Methylquinolin-2
authors J.Noeske, W.Shu, C.Bellamacina
compound source
Molecule: Dna Topoisomerase 4 Subunit B,Dna Topoisomerase ( Hydrolyzing) Chimera;
Chain: B, D, F, H
Fragment: Pare Ctd (Unp Residues 390-631) + Ef Linker + Par Residues 1-490) + Lehhhhhh;
Synonym: Topoisomerase Iv Subunit B
Ec: 5.6.2.2,5.6.2.2
Engineered: Yes
Organism_scientific: Klebsiella Pneumoniae 342
Organism_taxid: 507522
Strain: 342
Gene: Pare, Nctc5052_03997, Parc_1, Nctc5047_02751
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Dna (5'-D(Tptpapcpgptptpgptpapt)-3')
Chain: I, L, M, P
Engineered: Yes

Synthetic: Yes
Organism_scientific: Klebsiella Pneumoniae 342
Organism_taxid: 507522

Molecule: Dna (5'-D(Gpaptpcpaptpapcpapapcpgptp 3');
Chain: J, K, N, O
Engineered: Yes

Synthetic: Yes
Organism_scientific: Klebsiella Pneumoniae 342
Organism_taxid: 507522
symmetry Space Group: P 1 21 1
R_factor 0.274 R_Free 0.301
crystal
cell
length a length b length c angle alpha angle beta angle gamma
94.590 157.481 144.060 90.00 94.93 90.00
method X-Ray Diffractionresolution 3.20 Å
ligand CL, MG, MPD, PTR, TNJ enzyme Isomerase E.C.5.6.2.2 BRENDA
Primary referenceTopoisomerase Inhibitors Addressing Fluoroquinolone Resistance in Gram-Negative Bacteria., Skepper CK, Armstrong D, Balibar CJ, Bauer D, Bellamacina C, Benton BM, Bussiere D, De Pascale G, De Vicente J, Dean CR, Dhumale B, Fisher LM, Fuller J, Fulsunder M, Holder LM, Hu C, Kantariya B, Lapointe G, Leeds JA, Li X, Lu P, Lvov A, Ma S, Madhavan S, Malekar S, McKenney D, Mergo W, Metzger L, Moser HE, Mutnick D, Noeske J, Osborne C, Patel A, Patel D, Patel T, Prajapati K, Prosen KR, Reck F, Richie DL, Rico A, Sanderson MR, Satasia S, Sawyer WS, Selvarajah J, Shah N, Shanghavi K, Shu W, Thompson KV, Traebert M, Vala A, Vala L, Veselkov DA, Vo J, Wang M, Widya M, Williams SL, Xu Y, Yue Q, Zang R, Zhou B, Rivkin A, J Med Chem. 2020 Jul 23;63(14):7773-7816. doi: 10.1021/acs.jmedchem.0c00347. Epub, 2020 Jul 7. PMID:32634310
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (1283 Kb) [Save to disk]
  • Biological Unit Coordinates (6waa.pdb1.gz) 620 Kb
  • Biological Unit Coordinates (6waa.pdb2.gz) 646 Kb
  • LPC: Ligand-Protein Contacts for 6WAA
  • CSU: Contacts of Structural Units for 6WAA
  • Structure Factors (2042 Kb)
  • Retrieve 6WAA in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 6WAA from S2C, [Save to disk]
  • View 6WAA 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 6WAA
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [6waa_I] [6waa_L] [6waa_H] [6waa_J] [6waa_O] [6waa_M] [6waa_D] [6waa_P] [6waa_K] [6waa_B] [6waa_N] [6waa_F]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 6WAA
  • Community annotation for 6WAA at PDBWiki (http://pdbwiki.org)

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