5UKF Transferase Transferase Inhibitor date Jan 22, 2017
title Crystal Structure Of The Human Vaccinia-Related Kinase 1 Bou Oxindole Inhibitor
authors R.M.Counago, C.Wells, W.Zuercher, T.M.Willson, C.Bountra, A.M.Edw P.Arruda, O.Gileadi, Structural Genomics Consortium (Sgc)
compound source
Molecule: Serinethreonine-Protein Kinase Vrk1
Chain: A, B, C, D
Fragment: Unp Residues 3-364
Synonym: Vaccinia-Related Kinase 1
Ec: 2.7.11.1
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Vrk1
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_variant: R3
symmetry Space Group: P 21 21 21
R_factor 0.177 R_Free 0.214
crystal
cell
length a length b length c angle alpha angle beta angle gamma
92.138 96.051 192.741 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.40 Å
ligand 8E1, CL, PEG, PO4 enzyme Transferase E.C.2.7.11.1 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, D, C, B


Primary referenceStructural characterization of human Vaccinia-Related Kinases (VRK) bound to small-molecule inhibitors identifies different P-loop conformations., Counago RM, Allerston CK, Savitsky P, Azevedo H, Godoi PH, Wells CI, Mascarello A, de Souza Gama FH, Massirer KB, Zuercher WJ, Guimaraes CRW, Gileadi O, Sci Rep. 2017 Aug 8;7(1):7501. doi: 10.1038/s41598-017-07755-y. PMID:28790404
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (414 Kb) [Save to disk]
  • Biological Unit Coordinates (5ukf.pdb1.gz) 111 Kb
  • Biological Unit Coordinates (5ukf.pdb2.gz) 94 Kb
  • Biological Unit Coordinates (5ukf.pdb3.gz) 112 Kb
  • Biological Unit Coordinates (5ukf.pdb4.gz) 96 Kb
  • LPC: Ligand-Protein Contacts for 5UKF
  • CSU: Contacts of Structural Units for 5UKF
  • Structure Factors (2875 Kb)
  • Retrieve 5UKF in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5UKF from S2C, [Save to disk]
  • Re-refined 5ukf structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5UKF 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 5UKF
  • 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
  • Fold representative 5ukf from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5ukf_A] [5ukf_D] [5ukf] [5ukf_B] [5ukf_C]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5UKF
  • Community annotation for 5UKF at PDBWiki (http://pdbwiki.org)

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