6YTD Transferase date Apr 24, 2020
title Clk1 V324a Mutant Bound With Benzothiazole Tg003 (Cpd 2)
authors M.Schroeder, A.Chaikuad, S.Knapp, Structural Genomics Consortiu
compound source
Molecule: Dual Specificity Protein Kinase Clk1
Chain: A
Synonym: Cdc-Like Kinase 1
Ec: 2.7.12.1
Engineered: Yes
Mutation: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Clk1, Clk
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: I 1 2 1
R_factor 0.179 R_Free 0.228
crystal
cell
length a length b length c angle alpha angle beta angle gamma
80.917 64.702 89.344 90.00 114.74 90.00
method X-Ray Diffractionresolution 2.00 Å
ligand EAE enzyme Transferase E.C.2.7.12.1 BRENDA
Primary referenceDFG-1 Residue Controls Inhibitor Binding Mode and Affinity, Providing a Basis for Rational Design of Kinase Inhibitor Selectivity., Schroder M, Bullock AN, Fedorov O, Bracher F, Chaikuad A, Knapp S, J Med Chem. 2020 Sep 24;63(18):10224-10234. doi: 10.1021/acs.jmedchem.0c00898., Epub 2020 Aug 27. PMID:32787076
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (98 Kb) [Save to disk]
  • Biological Unit Coordinates (6ytd.pdb1.gz) 93 Kb
  • LPC: Ligand-Protein Contacts for 6YTD
  • CSU: Contacts of Structural Units for 6YTD
  • Structure Factors (1146 Kb)
  • Retrieve 6YTD in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 6YTD from S2C, [Save to disk]
  • View 6YTD 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 6YTD
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [6ytd_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 6YTD
  • Community annotation for 6YTD at PDBWiki (http://pdbwiki.org)

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