4UKD Transferase date May 20, 1997
title Umpcmp Kinase From Slime Mold Complexed With Adp, Udp, Bery Fluoride
authors I.Schlichting, J.Reinstein
compound source
Molecule: Uridylmonophosphatecytidylmonophosphate Kinase
Chain: A
Synonym: Umpcmp Kinase
Ec: 2.7.4.14
Engineered: Yes
Organism_scientific: Dictyostelium Discoideum
Organism_taxid: 44689
Strain: Ax2-214
Gene: Kcy_dicdi
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_plasmid: Pims5-Cduk-1
Expression_system_gene: Kcy_dicdi
symmetry Space Group: P 41 21 2
R_factor 0.194 R_Free 0.212
crystal
cell
length a length b length c angle alpha angle beta angle gamma
78.100 78.100 101.900 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.00 Å
ligand ADP, BF2, MG, UDP enzyme Transferase E.C.2.7.4.14 BRENDA
related structures by homologous chain: 2UKD, 3UKD
Gene KCY (D. discoideum)
Gene
Ontology
ChainFunctionProcessComponent
A
  • cytidylate kinase activity
  • UMP kinase activity


  • Primary referenceStructures of active conformations of UMP kinase from Dictyostelium discoideum suggest phosphoryl transfer is associative., Schlichting I, Reinstein J, Biochemistry 1997 Aug 5;36(31):9290-6. PMID:9280438
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (40 Kb) [Save to disk]
  • Biological Unit Coordinates (4ukd.pdb1.gz) 35 Kb
  • LPC: Ligand-Protein Contacts for 4UKD
  • CSU: Contacts of Structural Units for 4UKD
  • Likely Quarternary Molecular Structure file(s) for 4UKD
  • Structure Factors (183 Kb)
  • Retrieve 4UKD in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4UKD from S2C, [Save to disk]
  • Re-refined 4ukd structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4UKD 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 4UKD
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 4UKD, from MSDmotif at EBI
  • Genome occurence of 4UKD's fold from GeneCensus
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d4ukd__, region [Jmol] [rasmolscript] [script source]
  • Class (fold), Architecture (subfold), Topology, Homologous superfamily from CATH
  • Summaries and structural analyses of PDB data files from PDBSum
  • Identification of Protein Pockets & Cavities at CASTp
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4ukd_A] [4ukd]
  • SWISS-PROT database: [P20425]
  • Domain organization of [KCY_DICDI] by SWISSPFAM
  • Other resources with information on 4UKD
  • Community annotation for 4UKD 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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