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 
  • R-Value Observed: 0.157 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Peptidoglycan glycosyltransferaseA, B482Lancefieldella parvulum DSM 20469Mutation(s): 0 
Gene Names: Apar_1344
EC: 2.4.1.129
UniProt
Find proteins for C8W8H7 (Atopobium parvulum (strain ATCC 33793 / DSM 20469 / JCM 10300 / VPI 0546))
Explore C8W8H7 
Go to UniProtKB:  C8W8H7
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DXU (Subject of Investigation/LOI)
Query on DXU

Download Ideal Coordinates CCD File 
C [auth A], J [auth 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
C19 H25 Cl2 N3 O5 S
AXRWQAUUTZEPPM-YSIYDJFASA-N
 Ligand Interaction
P4G (Subject of Investigation/LOI)
Query on P4G

Download Ideal Coordinates CCD File 
D [auth A], E [auth A], F [auth A], K [auth B]1-ETHOXY-2-(2-ETHOXYETHOXY)ETHANE
C8 H18 O3
RRQYJINTUHWNHW-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

Download Ideal Coordinates CCD File 
G [auth A], H [auth A], I [auth A], L [auth B], M [auth B]1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, BL-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 
  • R-Value Observed: 0.157 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 67.611α = 90
b = 69.882β = 96.87
c = 114.251γ = 90
Software Package:
Software NamePurpose
Blu-Icedata collection
PHASERphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

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