6X6R

Crystal structure of C.difficile ribosyltransferase CDTa in complex with pCl-phenylthioDADMeImmA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.02 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.174 

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Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history


Literature

Crystal structure of C.difficile ribosyltransferase CDTa in complex with pCl-phenylthioDADMeImmA

Pozharski, E.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ADP-ribosyltransferaseA, B420Clostridioides difficileMutation(s): 0 
Gene Names: cdtA
UniProt
Find proteins for F5B5W8 (Clostridioides difficile)
Explore F5B5W8 
Go to UniProtKB:  F5B5W8
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
AR6 (Subject of Investigation/LOI)
Query on AR6

Download Ideal Coordinates CCD File 
D [auth B][(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL [HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL] HYDROGEN PHOSPHATE
C15 H23 N5 O14 P2
SRNWOUGRCWSEMX-ZQSHOCFMSA-N
 Ligand Interaction
4CT (Subject of Investigation/LOI)
Query on 4CT

Download Ideal Coordinates CCD File 
C [auth A], E [auth B](3R,4S)-1-[(4-amino-5H-pyrrolo[3,2-d]pyrimidin-7-yl)methyl]-4-{[(4-chlorophenyl)sulfanyl]methyl}pyrrolidin-3-ol
C18 H20 Cl N5 O S
MZZBHZOHYGEGEE-DOMZBBRYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.02 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.174 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 154.442α = 90
b = 76.066β = 122.1
c = 100.227γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

  • Deposited Date: 2020-05-29 
  • Released Date: 2021-10-13 
  • Deposition Author(s): Pozharski, E.

Revision History  (Full details and data files)

  • Version 1.0: 2021-10-13
    Type: Initial release