5XB3 Transferase date Mar 15, 2017
title Adp-Dtmp Bound Crystal Structure Of Thymidylate Kinase (Aq_9 Aquifex Aeolicus Vf5
authors A.Biswas, J.Jeyakanthan, K.Sekar
compound source
Molecule: Thymidylate Kinase
Chain: A, B
Synonym: Dtmp Kinase
Ec: 2.7.4.9
Engineered: Yes
 Organism_scientific: Aquifex Aeolicus (Strain Vf5)
Organism_taxid: 224324
Strain: Vf5
Gene: Tmk, Aq_969
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: P 1
R_factor 0.163 R_Free 0.213
crystal
cell
length a length b length c angle alpha angle beta angle gamma
42.540 52.980 53.780 90.97 90.69 109.60
method X-Ray Diffractionresolution 1.77 Å
ligand ADP, TMP enzyme Transferase E.C.2.7.4.9 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, B
  • thymidylate kinase activity
  • uridylate kinase activity


    • Primary referenceStructural studies of a hyperthermophilic thymidylate kinase enzyme reveal conformational substates along the reaction coordinate., Biswas A, Shukla A, Chaudhary SK, Santhosh R, Jeyakanthan J, Sekar K, FEBS J. 2017 Aug;284(15):2527-2544. doi: 10.1111/febs.14140. Epub 2017 Jul 13. PMID:28627020
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (75 Kb) [Save to disk]
  • Biological Unit Coordinates (5xb3.pdb1.gz) 69 Kb
  • LPC: Ligand-Protein Contacts for 5XB3
  • CSU: Contacts of Structural Units for 5XB3
  • Structure Factors (1583 Kb)
  • Retrieve 5XB3 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5XB3 from S2C, [Save to disk]
  • Re-refined 5xb3 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 5XB3 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 5XB3
  • Ramachandran plot from PDBSum
    • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1n5xb3, region B:537-694 [Jmol] [rasmolscript] [script source]
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5xb3_A] [5xb3_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 5XB3
  • Community annotation for 5XB3 at PDBWiki (http://pdbwiki.org)

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