2XCS

THE 2.1A CRYSTAL STRUCTURE OF S. AUREUS GYRASE COMPLEX WITH GSK299423 AND DNA

Structural Biology Knowledgebase: 2XCS SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.214
  • R-Value Work: 0.183

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 2XCS

Classification: ISOMERASE

Total Structure Weight: 169100.80


Macromolecule Entities
Molecule Chains Length Organism Details
DNA GYRASE SUBUNIT B, DNA GYRASE SUBUNIT A B, D 692 Staphylococcus aureus EC#: 5.99.1.3 IUBMB
Fragment: GYRB- C-TERMINAL 27KDA DOMAIN, RESIDUES 410-543 AND 580-644, GYRA- N-TERMINAL 56KDA DOMAIN, RESIDUES 2-491
Mutation: Y1123F
Details: C-TERMINUS GYRB (644) FUSED TO N-TERMINUS GYRA (1002). GREEK KEY DOMAIN (544-579) DELETED AND REPLACED WITH TWO RESIDUES, TG
Gene Name(s): gyrB SA0005 gyrA SA0006
Macromolecule Entities
Molecule Chains Length Organism Details
5'-5UA*D(GP*CP*CP*GP*TP*AP*GP*GP*GP*CP*CP *CP*TP*AP*CP*GP*GP*CP*T)-3' E, F 20 Synthetic construct

Small Molecules
Ligands 2 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
RXV
Query on RXV

F 6-METHOXY-4-(2-{4-[([1,3]OXATHIOLO[5,4-C]PYRIDIN- 6-YLMETHYL)AMINO]PIPERIDIN-1-YL}ETHYL)QUINOLINE- 3-CARBONITRILE
C25 H27 N5 O2 S
NKXJSCXEAVZSMF-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MN
Query on MN

B, D, E MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
RXV N/A in BindingDB
N/A in BindingMoad
IC50: 14 nM  PDBbind
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
5UA
Query on 5UA
E, F DNA LINKING C11 H13 N5 O5 --

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.214
  • R-Value Work: 0.183
  • Space Group: P 61
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 93.32 α = 90.00
b = 93.32 β = 90.00
c = 412.81 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2010-04-25
  • Released Date: 2010-08-04
  • Deposition author(s): Bax, B.D., Chan, P.F., Eggleston, D.S., Fosberry, A., Gentry, D.R., Gorrec, F., Giordano, I., Hann, M.M., Hennessy, A., Hibbs, M., Huang, J., Jones, E., Jones, J., Brown, K.K., Lewis, C.J., May, E.W., Singh, O., Spitzfaden, C., Shen, C., Shillings, A., Theobald, A.F., Wohlkonig, A., Pearson, N.D., Gwynn, M.N.

Revision History

  • 2011-09-28
    Type: Citation | Details: JRNL