2X9F Transferase date Mar 17, 2010
title Ephb4 Kinase Domain Inhibitor Complex
authors J.Read, C.A.Brassington, I.Green, E.J.Mccall, A.L.Valentine, D.B
compound source
Molecule: Ephrin Type-B Receptor 4
Chain: A
Fragment: Kinase Domain, Residues 598-899
Synonym: Ephb4 Receptor Tyrosine Kinase, Tyrosine-Protein K Receptor Htk, Tyrosine-Protein Kinase Tyro11;
Ec: 2.7.10.1
Engineered: Yes
Mutation: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Spodoptera Frugiperda
Expression_system_taxid: 7108
Expression_system_cell_line: Sf21
Expression_system_vector_type: Baculovirus
Expression_system_plasmid: Pfastbac
symmetry Space Group: P 1 21 1
R_factor 0.15675 R_Free 0.19422
crystal
cell
length a length b length c angle alpha angle beta angle gamma
47.120 52.479 61.369 90.00 112.05 90.00
method X-Ray Diffractionresolution 1.75 Å
ligand MG, X9F BindingDB enzyme Transferase E.C.2.7.10.1 BRENDA
Primary referenceInhibitors of the tyrosine kinase EphB4. Part 3: Identification of non-benzodioxole-based kinase inhibitors., Bardelle C, Barlaam B, Brooks N, Coleman T, Cross D, Ducray R, Green I, Brempt CL, Olivier A, Read J, Bioorg Med Chem Lett. 2010 Sep 15. PMID:20850301
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (95 Kb) [Save to disk]
  • Biological Unit Coordinates (2x9f.pdb1.gz) 90 Kb
  • LPC: Ligand-Protein Contacts for 2X9F
  • CSU: Contacts of Structural Units for 2X9F
  • Structure Factors (354 Kb)
  • Retrieve 2X9F in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2X9F from S2C, [Save to disk]
  • Re-refined 2x9f structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2X9F 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 2X9F
  • 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 2X9F, from MSDmotif at EBI
  • Fold representative 2x9f from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2x9f_A] [2x9f]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 2X9F: [TyrKc ] by SMART
  • Alignments of the sequence of 2X9F with the sequences similar proteins can be viewed for 2X9F's classification at ProtoMap. Click on "Neighbors List", then on the "See Alignments" button below the list.
  • A sequence distance tree ("phylogenetic tree") can be viewed for 1ACL's classification at ProtoMap. Click on the Cluster number.
  • Other resources with information on 2X9F
  • Community annotation for 2X9F at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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