5VD3 Transferase Transferase Inhibitor date Apr 01, 2017
title Crystal Structure Of Human Myt1 Kinase Domain (De-Phosphoryl Complex With Saracatinib
authors J.Y.Zhu, E.Schonbrunn
compound source
Molecule: Membrane-Associated Tyrosine- And Threonine-Speci Inhibitory Kinase;
Chain: A
Fragment: Kinase Domain, Unp Residues 75-362
Synonym: Myt1 Kinase
Ec: 2.7.11.1
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Pkmyt1, Myt1
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)-Ripl
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pnic28-Bsa4
symmetry Space Group: P 21 21 21
R_factor 0.166 R_Free 0.204
crystal
cell
length a length b length c angle alpha angle beta angle gamma
47.040 54.060 114.110 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.80 Å
ligand EDO, H8H, PEG enzyme Transferase E.C.2.7.11.1 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceStructural basis of Wee kinases functionality and inactivation by diverse small molecule inhibitors., Zhu JY, Cuellar RAD, Berndt N, Lee HE, Olesen SH, Martin MP, Jensen JT, Georg GI, Schonbrunn E, J Med Chem. 2017 Aug 9. doi: 10.1021/acs.jmedchem.7b00996. PMID:28792760
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (146 Kb) [Save to disk]
  • Biological Unit Coordinates (5vd3.pdb1.gz) 140 Kb
  • LPC: Ligand-Protein Contacts for 5VD3
  • CSU: Contacts of Structural Units for 5VD3
  • Structure Factors (220 Kb)
  • Retrieve 5VD3 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5VD3 from S2C, [Save to disk]
  • View 5VD3 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 5VD3
  • 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
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5vd3_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5VD3
  • Community annotation for 5VD3 at PDBWiki (http://pdbwiki.org)

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