5P9F Transferase date Sep 20, 2016
title Btk In Complex With Gdc-0834
authors A.S.Gardberg
compound source
Molecule: Tyrosine-Protein Kinase Btk
Chain: A
Fragment: Kinase Domain
Synonym: Agammaglobulinemia Tyrosine Kinase,Atk,B-Cell Prog Kinase,Bpk,Bruton Tyrosine Kinase;
Ec: 2.7.10.2
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Btk, Agmx1, Atk, Bpk
Expression_system: Trichoplusia Ni
Expression_system_taxid: 7111
Expression_system_strain: Hi5
symmetry Space Group: P 21 21 2
R_factor 0.150 R_Free 0.223
crystal
cell
length a length b length c angle alpha angle beta angle gamma
72.911 103.931 38.612 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.71 Å
ligand 2VL, EDO, GOL enzyme Transferase E.C.2.7.10.2 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceAbility of Bruton's Tyrosine Kinase Inhibitors to Sequester Y551 and Prevent Phosphorylation Determines Potency for Inhibition of Fc Receptor but not B-Cell Receptor Signaling., Bender AT, Gardberg A, Pereira A, Johnson T, Wu Y, Grenningloh R, Head J, Morandi F, Haselmayer P, Liu-Bujalski L, Mol Pharmacol. 2017 Mar;91(3):208-219. doi: 10.1124/mol.116.107037. Epub 2017 Jan, 6. PMID:28062735
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (105 Kb) [Save to disk]
  • Biological Unit Coordinates (5p9f.pdb1.gz) 98 Kb
  • LPC: Ligand-Protein Contacts for 5P9F
  • CSU: Contacts of Structural Units for 5P9F
  • Structure Factors (278 Kb)
  • Retrieve 5P9F in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5P9F from S2C, [Save to disk]
  • Re-refined 5p9f structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5P9F 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 5P9F
  • 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: [5p9f] [5p9f_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5P9F
  • Community annotation for 5P9F at PDBWiki (http://pdbwiki.org)

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