5NPK Isomerase date Apr 17, 2017
title 1.98a Structure Of Thiophene1 With S.Aureus Dna Gyrase And D
authors B.D.Bax, P.F.Chan, R.A.Stavenger
compound source
Molecule: Dna Gyrase Subunit B,Dna Gyrase Subunit B,Dna Gyr Subunit A;
Chain: B, D, b, d
Engineered: Yes
Organism_scientific: Staphylococcus Aureus
Organism_taxid: 158879
Strain: N315
Gene: Gyrb, Sa0005, Gyra, Sa0006
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Dna (5'- D(Apgpcpcpgptpapgpgptpapcpcptpapcpgpgpcp
Chain: E, F, e, f
Engineered: Yes

Organism_scientific: Synthetic Construct
Organism_taxid: 32630
Expression_system: Synthetic Construct
Expression_system_taxid: 32630
symmetry Space Group: P 1 21 1
R_factor 0.154 R_Free 0.183
length a length b length c angle alpha angle beta angle gamma
89.442 120.680 168.899 90.00 90.05 90.00
method X-Ray Diffractionresolution 1.98 Å
ligand 94H, 9JN, CL, GOL, MN, NA, SO4 enzyme Isomerase E.C. BRENDA
b, D, d, B

Primary referenceThiophene antibacterials that allosterically stabilize DNA-cleavage complexes with DNA gyrase., Chan PF, Germe T, Bax BD, Huang J, Thalji RK, Bacque E, Checchia A, Chen D, Cui H, Ding X, Ingraham K, McCloskey L, Raha K, Srikannathasan V, Maxwell A, Stavenger RA, Proc Natl Acad Sci U S A. 2017 May 30;114(22):E4492-E4500. doi:, 10.1073/pnas.1700721114. Epub 2017 May 15. PMID:28507124
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (1050 Kb) [Save to disk]
  • Biological Unit Coordinates (5npk.pdb1.gz) 514 Kb
  • Biological Unit Coordinates (5npk.pdb2.gz) 528 Kb
  • LPC: Ligand-Protein Contacts for 5NPK
  • CSU: Contacts of Structural Units for 5NPK
  • Structure Factors (3940 Kb)
  • Retrieve 5NPK in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5NPK from S2C, [Save to disk]
  • Re-refined 5npk structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5NPK 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 5NPK
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • Fold representative 5npk from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5npk_D] [5npk_B] [5npk_d] [5npk_E] [5npk_e] [5npk_f] [5npk_b] [5npk_F]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5NPK
  • Community annotation for 5NPK at PDBWiki (http://pdbwiki.org)

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