4R3J

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.44 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.171 

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 cefapirin

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
CFU
Query on CFU

Download SDF File 
Download CCD File 
A, B
(2R)-2-[(1R)-1-(acetylamino)-2-oxoethyl]-5-methyl-3,6-dihydro-2H-1,3-thiazine-4-carboxylic acid
C10 H14 N2 O4 S
POOBXVPMJBGTRO-VXNVDRBHSA-N
 Ligand Interaction
PO4
Query on PO4

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Download CCD File 
A, B
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
GOL
Query on GOL

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Download CCD File 
A, B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-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: 2.44 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.171 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 99.633α = 90.00
b = 119.836β = 90.00
c = 82.544γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
REFMACrefinement
Blu-Icedata collection

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