1DY3

Ternary complex of 7,8-dihydro-6-hydroxymethylpterinpyrophosphokinase from Escherichia coli with ATP and a substrate analogue.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Work: 0.165 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

2.0A X-Ray Structure of the Ternary Complex of 7,8-Dihydro-6-Hydroxymethylpterinpyrophosphokinase from Escherichia Coli with ATP and a Substrate Analogue

Stammers, D.K.Achari, A.Somers, D.O.Bryant, P.K.Rosemond, J.Scott, D.L.Champness, J.N.

(1999) FEBS Lett 456: 49

  • DOI: 10.1016/s0014-5793(99)00860-1
  • Primary Citation of Related Structures:  
    1DY3

  • PubMed Abstract: 
  • The X-ray crystal structure of 7,8-dihydro-6-hydroxymethylpterinpyrophosphokinase (PPPK) in a ternary complex with ATP and a pterin analogue has been solved to 2.0 A resolution, giving, for the first time, detailed information of the PPPK/ATP intermolecular interactions and the accompanying conformational change ...

    The X-ray crystal structure of 7,8-dihydro-6-hydroxymethylpterinpyrophosphokinase (PPPK) in a ternary complex with ATP and a pterin analogue has been solved to 2.0 A resolution, giving, for the first time, detailed information of the PPPK/ATP intermolecular interactions and the accompanying conformational change. The first 100 residues of the 158 residue peptide contain a betaalpha betabeta alphabeta motif present in several other proteins including nucleoside diphosphate kinase. Comparative sequence examination of a wide range of prokaryotic and lower eukaryotic species confirms the conservation of the PPPK active site, indicating the value of this de novo folate biosynthesis pathway enzyme as a potential target for the development of novel broad-spectrum anti-infective agents.


    Organizational Affiliation

    Glaxo Wellcome R&D, Medicines Research Centre, Stevenage, UK.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
N/AA158Escherichia coliMutation(s): 0 
EC: 2.7.6.3
UniProt
Find proteins for P26281 (Escherichia coli (strain K12))
Explore P26281 
Go to UniProtKB:  P26281
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ATP (Subject of Investigation/LOI)
Query on ATP

Download Ideal Coordinates CCD File 
B [auth A]ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
 Ligand Interaction
87Y (Subject of Investigation/LOI)
Query on 87Y

Download Ideal Coordinates CCD File 
C [auth A]7,8-DIHYDRO-6-HYDROXYMETHYL-7-METHYL-7-[2-PHENYLETHYL]-PTERIN
C16 H19 N5 O2
XMFJTCGUDFSWSW-INIZCTEOSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
D [auth A], E [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Work: 0.165 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 40.96α = 90
b = 69.01β = 90
c = 115.49γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2000-08-18
    Type: Initial release
  • Version 1.1: 2011-05-07
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance