3OP5 Transferase date Aug 31, 2010
title Human Vaccinia-Related Kinase 1
authors C.K.Allerston, S.Uttarkar, P.Savitsky, J.M.Elkins, P.Filippakopo T.Krojer, P.Rellos, O.Fedorov, J.Eswaran, B.Brenner, T.Keates, S. O.King, R.Chalk, G.Berridge, F.Von Delft, O.Gileadi, C.H.Arrowsm A.M.Edwards, J.Weigelt, C.Bountra, S.Knapp, Structural Genomics Consortium (Sgc)
compound source
Molecule: Serinethreonine-Protein Kinase Vrk1
Chain: A, B, C, D
Fragment: Kinase Domain, Residues 3-369
Synonym: Vaccinia-Related Kinase 1
Engineered: Yes
Mutation: 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)-R3-Prare2
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pnic28-Bsa4
symmetry Space Group: P 21 21 21
R_factor 0.178 R_Free 0.213
length a length b length c angle alpha angle beta angle gamma
92.970 97.190 191.990 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.40 Å
ligand EDO, GOL, REB enzyme Transferase E.C. BRENDA
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] (438 Kb) [Save to disk]
  • Biological Unit Coordinates (3op5.pdb1.gz) 112 Kb
  • Biological Unit Coordinates (3op5.pdb2.gz) 114 Kb
  • Biological Unit Coordinates (3op5.pdb3.gz) 109 Kb
  • Biological Unit Coordinates (3op5.pdb4.gz) 106 Kb
  • LPC: Ligand-Protein Contacts for 3OP5
  • CSU: Contacts of Structural Units for 3OP5
  • Structure Factors (1427 Kb)
  • Retrieve 3OP5 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3OP5 from S2C, [Save to disk]
  • Re-refined 3op5 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3OP5 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 3OP5
  • 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 3OP5, from MSDmotif at EBI
  • Fold representative 3op5 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3op5_D] [3op5_C] [3op5_A] [3op5] [3op5_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 3OP5: [STYKc ] by SMART
  • Other resources with information on 3OP5
  • Community annotation for 3OP5 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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