4KQI

Crystal structure of CobT E317A complexed with its reaction products


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.173 
  • 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

Dissecting cobamide diversity through structural and functional analyses of the base-activating CobT enzyme of Salmonella enterica.

Chan, C.H.Newmister, S.A.Talyor, K.Claas, K.R.Rayment, I.Escalante-Semerena, J.C.

(2014) Biochim Biophys Acta 1840: 464-475

  • DOI: 10.1016/j.bbagen.2013.09.038
  • Primary Citation of Related Structures:  
    4KQF, 4KQG, 4KQH, 4KQI, 4KQJ, 4KQK

  • PubMed Abstract: 
  • Cobamide diversity arises from the nature of the nucleotide base. Nicotinate mononucleotide (NaMN):base phosphoribosyltransferases (CobT) synthesize α-linked riboside monophosphates from diverse nucleotide base substrates (e.g., benzimidazoles, purines, phenolics) that are incorporated into cobamides ...

    Cobamide diversity arises from the nature of the nucleotide base. Nicotinate mononucleotide (NaMN):base phosphoribosyltransferases (CobT) synthesize α-linked riboside monophosphates from diverse nucleotide base substrates (e.g., benzimidazoles, purines, phenolics) that are incorporated into cobamides.


    Organizational Affiliation

    Department of Bacteriology, University of Wisconsin, Madison, WI, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Nicotinate-nucleotide--dimethylbenzimidazole phosphoribosyltransferaseA356Salmonella enterica subsp. enterica serovar Typhimurium str. LT2Mutation(s): 1 
Gene Names: cobTSTM2016
EC: 2.4.2.21
UniProt
Find proteins for Q05603 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720))
Explore Q05603 
Go to UniProtKB:  Q05603
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ05603
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
RBZ
Query on RBZ

Download Ideal Coordinates CCD File 
B [auth A]ALPHA-RIBAZOLE-5'-PHOSPHATE
C14 H19 N2 O7 P
ZMRGXEJKZPRBPJ-SYQHCUMBSA-N
 Ligand Interaction
NIO
Query on NIO

Download Ideal Coordinates CCD File 
D [auth A]NICOTINIC ACID
C6 H5 N O2
PVNIIMVLHYAWGP-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

Download Ideal Coordinates CCD File 
C [auth A]1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.174 
  • Space Group: P 2 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.753α = 90
b = 71.278β = 90
c = 89.444γ = 90
Software Package:
Software NamePurpose
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-3000data collection
HKL-3000data reduction
SADABSdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-03-12
    Type: Initial release