4C8B Transferase date Sep 30, 2013
title Structure Of The Kinase Domain Of Human Ripk2 In Complex Wit Ponatinib
authors P.Canning, T.Krojer, A.Bradley, P.Mahajan, S.Goubin, F.Von Delft, C.H.Arrowsmith, A.M.Edwards, C.Bountra, A.Bullock
compound source
Molecule: Receptor-Interacting Serinethreonine-Protein Kin
Chain: A, B
Fragment: Kinase Domain, Residues 8-317
Synonym: Card-Containing Interleukin-1 Beta-Converting Enzy Associated Kinase, Card-Containing Il-1 Beta Ice-Kinase, Ri Interacting Clarp Kinase, Receptor-Interacting Protein 2, R Tyrosine-Protein Kinase Ripk2, Ripk2;
Ec: 2.7.11.1, 2.7.10.2
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Spodoptera Frugiperda
Expression_system_common: Fall Armyworm
Expression_system_taxid: 7108
Expression_system_vector_type: Baculovirus
symmetry Space Group: P 21 21 21
R_factor 0.201 R_Free 0.244
crystal
cell
length a length b length c angle alpha angle beta angle gamma
58.735 86.682 137.335 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.75 Å
ligand 0LI, EDO enzyme Transferase E.C.2.7.11.1 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, B


Primary referenceInflammatory Signaling by NOD-RIPK2 Is Inhibited by Clinically Relevant Type II Kinase Inhibitors., Canning P, Ruan Q, Schwerd T, Hrdinka M, Maki JL, Saleh D, Suebsuwong C, Ray S, Brennan PE, Cuny GD, Uhlig HH, Gyrd-Hansen M, Degterev A, Bullock AN, Chem Biol. 2015 Sep 17;22(9):1174-84. doi: 10.1016/j.chembiol.2015.07.017. Epub, 2015 Aug 27. PMID:26320862
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (192 Kb) [Save to disk]
  • Biological Unit Coordinates (4c8b.pdb1.gz) 184 Kb
  • LPC: Ligand-Protein Contacts for 4C8B
  • CSU: Contacts of Structural Units for 4C8B
  • Structure Factors (975 Kb)
  • Retrieve 4C8B in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4C8B from S2C, [Save to disk]
  • Re-refined 4c8b structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4C8B 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 4C8B
  • 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 4C8B, from MSDmotif at EBI
  • Fold representative 4c8b from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4c8b_B] [4c8b_A] [4c8b]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 4C8B: [STYKc ] by SMART
  • Other resources with information on 4C8B
  • Community annotation for 4C8B at PDBWiki (http://pdbwiki.org)

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