4R23

Structure of a putative peptidoglycan glycosyltransferase from Atopobium parvulum in complex with dicloxacillin

Structural Biology Knowledgebase: 4R23 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.84 Å
  • R-Value Free: 0.192
  • R-Value Work: 0.155

Literature

Macromolecules
Sequence Display for 4R23

Classification: TRANSFERASE / TRANSFERASE INHIBITOR

Total Structure Weight: 103214.76

Macromolecule Entities
Molecule Chains Length Organism Details
Peptidoglycan glycosyltransferase A, B 482 Atopobium parvulum EC#: 2.4.1.129 IUBMB
Fragment: Residues 505-954
Gene Name(s): Apar_1344
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

A, B (3R,4R,5R)-3-(2,6-dichlorophenyl)-N-{(1R)- 1-[(2R,4S)-4-(dihydroxymethyl)-5,5-dimethyl- 1,3-thiazolidin-2-yl]-2-oxoethyl}-5-methyl- 1,2-oxazolidine-4-carboxamide
dicloxacillin - open form (Synonym)
C19 H25 Cl2 N3 O5 S
AXRWQAUUTZEPPM-YSIYDJFASA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
P4G
Query on P4G

A, B 1-ETHOXY-2-(2-ETHOXYETHOXY)ETHANE
C8 H18 O3
RRQYJINTUHWNHW-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
EDO
Query on EDO

A, B 1,2-ETHANEDIOL
ETHYLENE GLYCOL (Synonym)
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
MSE
Query on MSE
A, B L-PEPTIDE LINKING C5 H11 N O2 Se MET

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.84 Å
  • R-Value Free: 0.192
  • R-Value Work: 0.155
  • Space Group: P 1 21 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 67.61 α = 90.00
b = 69.88 β = 96.87
c = 114.25 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2014-08-08
  • Released Date: 2014-09-17
  • Deposition author(s): Filippova, E.V., Minasov, G., Kiryukhina, O., Clancy, S., Joachimiak, A., Anderson, W.F., Midwest Center for Structural Genomics (MCSG)

Revision History

No revisions since initial release