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 
  • R-Value Observed: 0.176 

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Ligand Structure Quality Assessment 


This is version 1.6 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: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Peptidoglycan glycosyltransferase
A, B
482Lancefieldella parvula DSM 20469Mutation(s): 0 
Gene Names: Apar_1344
EC: 2.4.1.129
UniProt
Find proteins for C8W8H7 (Lancefieldella parvula (strain ATCC 33793 / DSM 20469 / CCUG 32760 / JCM 10300 / KCTC 3663 / VPI 0546 / 1246))
Explore C8W8H7 
Go to UniProtKB:  C8W8H7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupC8W8H7
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
35P
Query on 35P
Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]		(2R,4S)-5,5-dimethyl-2-{(1R)-2-oxo-1-[(phenoxyacetyl)amino]ethyl}-1,3-thiazolidine-4-carboxylic acid
C16 H20 N2 O5 S
OQVOJWZOUWGSDX-KWCYVHTRSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D 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
b = 70.019β = 96.93
c = 114.625γ = 90
Software Package:
Software NamePurpose
Blu-Icedata collection
PHASERphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-07-09
    Type: Initial release
  • Version 1.1: 2014-08-13
    Changes: Database references, Structure summary
  • Version 1.2: 2015-08-12
    Changes: Non-polymer description
  • Version 1.3: 2017-11-22
    Changes: Refinement description
  • Version 1.4: 2018-01-24
    Changes: Database references
  • Version 1.5: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.6: 2023-12-06
    Changes: Data collection