2WK5

Structural features of native human thymidine phosphorylase and in complex with 5-iodouracil

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.99 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.207 

Starting Model: experimental
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This is version 1.3 of the entry. See complete history. 


Literature

Structures of Native Human Thymidine Phosphorylase and in Complex with 5-Iodouracil.

Mitsiki, E., Papageorgiou, A.C., Iyer, S., Thiyagarajan, N., Prior, S.H., Sleep, D., Finnis, C., Acharya, K.R.

(2009) Biochem Biophys Res Commun 386: 666

  • DOI: https://doi.org/10.1016/j.bbrc.2009.06.104
  • Primary Citation of Related Structures:  
    2WK5, 2WK6

  • PubMed Abstract: 

    Thymidine phosphorylase (TP) first identified as platelet derived endothelial cell growth factor (PD-ECGF) plays a key role in nucleoside metabolism. Human TP (hTP) is implicated in angiogenesis and is overexpressed in several solid tumors. Here, we report the crystal structures of recombinant hTP and its complex with a substrate 5-iodouracil (5IUR) at 3.0 and 2.5A, respectively. In addition, we provide information on the role of specific residues in the enzymatic activity of hTP through mutagenesis and kinetic studies.

    • Organizational Affiliation: 

    Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath BA2 7AY, UK.


Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
THYMIDINE PHOSPHORYLASE
A, B, C, D
482Homo sapiensMutation(s): 0 
EC: 2.4.2.4
UniProt & NIH Common Fund Data Resources
Find proteins for P19971 (Homo sapiens)
Explore P19971 
Go to UniProtKB:  P19971
PHAROS:  P19971
GTEx:  ENSG00000025708 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP19971
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL
Download Ideal Coordinates CCD File 
E [auth B]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.99 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.207 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 103.532α = 90
b = 77.188β = 98.04
c = 100.878γ = 90
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-07-07
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-12-13
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description