4QJG

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.175 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

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

Filippova, E.V.Minasov, G.Kiryukhina, O.Clancy, S.Joachimiak, A.Anderson, W.F.Midwest Center for Structural Genomics (MCSG)

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 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
35P
Query on 35P

Download SDF File 
Download CCD File 
A, B
(2R,4S)-5,5-dimethyl-2-{(1R)-2-oxo-1-[(phenoxyacetyl)amino]ethyl}-1,3-thiazolidine-4-carboxylic acid
OPEN FORM - PENICILLIN V
C16 H20 N2 O5 S
OQVOJWZOUWGSDX-KWCYVHTRSA-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

Unit Cell:
Length (Å)Angle (°)
a = 66.723α = 90.00
b = 70.019β = 96.93
c = 114.625γ = 90.00
Software Package:
Software NamePurpose
Blu-Icedata collection
HKL-2000data reduction
REFMACrefinement
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-07-09
    Type: Initial release
  • Version 1.1: 2014-08-13
    Type: Database references, Structure summary
  • Version 1.2: 2015-08-12
    Type: Non-polymer description
  • Version 1.3: 2017-11-22
    Type: Refinement description
  • Version 1.4: 2018-01-24
    Type: Database references