4R23

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


Experimental Data Snapshot

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

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

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

Filippova, E.V.Minasov, G.Kiryukhina, O.Clancy, S.Joachimiak, A.Anderson, W.F.

To be published.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Peptidoglycan glycosyltransferase
A, B
482Atopobium parvulum (strain ATCC 33793 / DSM 20469 / JCM 10300 / VPI 0546)Mutation(s): 0 
EC: 2.4.1.129
Find proteins for C8W8H7 (Atopobium parvulum (strain ATCC 33793 / DSM 20469 / JCM 10300 / VPI 0546))
Go to UniProtKB:  C8W8H7
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DXU
Query on DXU

Download SDF File 
Download CCD File 
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
C19 H25 Cl2 N3 O5 S
AXRWQAUUTZEPPM-YSIYDJFASA-N
 Ligand Interaction
EDO
Query on EDO

Download SDF File 
Download CCD File 
A, B
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
P4G
Query on P4G

Download SDF File 
Download CCD File 
A, B
1-ETHOXY-2-(2-ETHOXYETHOXY)ETHANE
C8 H18 O3
RRQYJINTUHWNHW-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
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
Unit Cell:
Length (Å)Angle (°)
a = 67.611α = 90.00
b = 69.882β = 96.87
c = 114.251γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
Blu-Icedata collection
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-09-17
    Type: Initial release
  • Version 1.1: 2017-11-22
    Type: Refinement description