4R0Q

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.179 

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 cephalothin

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
SCN
Query on SCN

Download SDF File 
Download CCD File 
A, B
THIOCYANATE ION
C N S
ZMZDMBWJUHKJPS-UHFFFAOYSA-M
 Ligand Interaction
B3P
Query on B3P

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Download CCD File 
A, B
2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C11 H26 N2 O6
HHKZCCWKTZRCCL-UHFFFAOYSA-N
 Ligand Interaction
CEP
Query on CEP

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Download CCD File 
A, B
CEPHALOTHIN GROUP
C16 H18 N2 O6 S2
UUWFGEKEQSCSMB-IAQYHMDHSA-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 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.179 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 68.553α = 90.00
b = 70.002β = 96.76
c = 115.233γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data scaling
HKL-2000data reduction
PHASERphasing
Blu-Icedata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-08-27
    Type: Initial release
  • Version 1.1: 2017-11-22
    Type: Refinement description