2J0F Transferase date Aug 02, 2006
title Structural Basis For Non-Competitive Product Inhibition In Human Thymidine Phosphorylase: Implication For Drug Design
authors K.El Omari, A.Bronckaers, S.Liekens, M.J.Perez-Perez, J.Balzarini, D.K.Stammers
compound source
Molecule: Thymidine Phosphorylase
Chain: A, B, C, D
Synonym: Tdrpase, Tp, Platelet-Derived Endothelial Cell Growth Factor, Gliostatin, Pd-Ecgf;
Ec: 2.4.2.4
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: P 1 21 1
R_factor 0.246 R_Free 0.287
crystal
cell
length a length b length c angle alpha angle beta angle gamma
103.078 76.087 99.575 90.00 98.61 90.00
method X-Ray Diffractionresolution 2.31 Å
ligand TDR enzyme Transferase E.C.2.4.2.4 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, D, C, B


Primary referenceStructural basis for non-competitive product inhibition in human thymidine phosphorylase: implications for drug design., El Omari K, Bronckaers A, Liekens S, Perez-Perez MJ, Balzarini J, Stammers DK, Biochem J. 2006 Oct 15;399(2):199-204. PMID:16803458
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (275 Kb) [Save to disk]
  • Biological Unit Coordinates (2j0f.pdb1.gz) 138 Kb
  • Biological Unit Coordinates (2j0f.pdb2.gz) 135 Kb
  • LPC: Ligand-Protein Contacts for 2J0F
  • CSU: Contacts of Structural Units for 2J0F
  • Likely Quarternary Molecular Structure file(s) for 2J0F
  • Structure Factors (488 Kb)
  • Retrieve 2J0F in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2J0F from S2C, [Save to disk]
  • Re-refined 2j0f structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2J0F in 3D
  • Proteopedia, because life has more than 2D.
  • On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.
  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
  • Visual 3D analysis of 2J0F
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Electron Density related parameters from EDS Electron Density Server, at Upsala
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 2J0F, from MSDmotif at EBI
  • Fold representative 2j0f from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2j0f] [2j0f_A] [2j0f_B] [2j0f_C] [2j0f_D]
  • SWISS-PROT database: [P19971]
  • Domain organization of [TYPH_HUMAN] by SWISSPFAM
  • Domain found in 2J0F: [PYNP_C ] by SMART
  • Alignments of the sequence of 2J0F with the sequences similar proteins can be viewed for 2J0F's classification [TYPH_HUMAN] at ProtoMap. Click on "Neighbors List", then on the "See Alignments" button below the list.
  • A sequence distance tree ("phylogenetic tree") can be viewed for 1ACL's classification [TYPH_HUMAN] at ProtoMap. Click on the Cluster number.
  • Other resources with information on 2J0F
  • Community annotation for 2J0F at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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