4RA7

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.94 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.161 

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 nafcillin

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
453Atopobium 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
NXU
Query on NXU

Download SDF File 
Download CCD File 
A, B
(2R,4S)-2-[(1R)-2-hydroxy-1-{[(2-hydroxynaphthalen-1-yl)carbonyl]amino}ethyl]-5,5-dimethyl-1,3-thiazolidine-4-carboxylic acid
C19 H22 N2 O5 S
BZLDRFAHCQLJIH-ISTRZQFTSA-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: 1.94 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.161 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 68.399α = 90.00
b = 70.059β = 96.97
c = 114.567γ = 90.00
Software Package:
Software NamePurpose
HKL-3000data scaling
REFMACrefinement
HKL-3000data reduction
Blu-Icedata collection
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-09-24
    Type: Initial release
  • Version 1.1: 2017-11-22
    Type: Refinement description