5YV8 Transferase date Nov 24, 2017
title Structure Of Camkk2 In Complex With Cki-002
authors H.Niwa, N.Handa, S.Yokoyama
compound source
Molecule: Calciumcalmodulin-Dependent Protein Kinase Kinas
Chain: A
Synonym: Camkk 2,Calciumcalmodulin-Dependent Protein Kinas Beta,Camkk Beta;
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Camkk2, Camkkb, Kiaa0787
Expression_system: Cell-Free Synthesis
Expression_system_taxid: 32644
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Px070406-05
symmetry Space Group: P 21 21 21
R_factor 0.164 R_Free 0.213
length a length b length c angle alpha angle beta angle gamma
66.493 76.969 83.895 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.93 Å
ligand 91L, CAS, CL, GOL enzyme Transferase E.C. BRENDA

Primary referenceProtein ligand interaction analysis against new CaMKK2 inhibitors by use of X-ray crystallography and the fragment molecular orbital (FMO) method., Takaya D, Niwa H, Mikuni J, Nakamura K, Handa N, Tanaka A, Yokoyama S, Honma T, J Mol Graph Model. 2020 Apr 10;99:107599. doi: 10.1016/j.jmgm.2020.107599. PMID:32348940
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (100 Kb) [Save to disk]
  • Biological Unit Coordinates (5yv8.pdb1.gz) 95 Kb
  • LPC: Ligand-Protein Contacts for 5YV8
  • CSU: Contacts of Structural Units for 5YV8
  • Structure Factors (1258 Kb)
  • Retrieve 5YV8 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5YV8 from S2C, [Save to disk]
  • View 5YV8 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 5YV8
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • Fold representative 5yv8 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5yv8_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5YV8
  • Community annotation for 5YV8 at PDBWiki (http://pdbwiki.org)

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