2WK6

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

PDB DOI: https://doi.org/10.2210/pdb2WK6/pdb

Classification: TRANSFERASE
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2009-06-05 Released: 2009-07-07
Deposition Author(s): Mitsiki, E., Papageorgiou, A.C., Iyer, S., Thiyagarajan, N., Prior, S.H., Sleep, D., Finnis, C., Acharya, K.R.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.283
R-Value Work: 0.227
R-Value Observed: 0.227

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 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

PubMed: 19555658 Search on PubMedSearch on PubMed Central
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.

Macromolecule Content

Total Structure Weight: 100.48 kDa
Atom Count: 6,576
Modelled Residue Count: 894
Deposited Residue Count: 964
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
THYMIDINE PHOSPHORYLASE	A, B	482	Homo sapiens	Mutation(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 Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P19971
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
IUR Query on IUR Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth B]	C [auth A], D [auth B]	5-IODOURACIL C₄ H₃ I N₂ O₂ KSNXJLQDQOIRIP-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Binding Affinity Annotations
ID	Source	Binding Affinity
IUR	PDBBind: 2WK6	Ki: 4.80e+5 (nM) from 1 assay(s)
IUR	Binding MOAD: 2WK6	Ki: 4.80e+5 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.283
R-Value Work: 0.227
R-Value Observed: 0.227
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.911	α = 90
b = 67.266	β = 90
c = 212.274	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2009-07-07

Deposition Author(s):

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: 2018-01-17
Changes: Data collection
Version 1.4: 2023-12-13
Changes: Data collection, Database references, Derived calculations, Other, Refinement description