2VWX Transferase date Jun 27, 2008
title Ephb4 Kinase Domain Inhibitor Complex
authors J.Read, C.A.Brassington, I.Green, E.J.Mccall, A.L.Valentine, D.Barratt, A.G.Leach, J.G.Kettle
compound source
Molecule: Ephrin Type-B Receptor 4
Chain: A
Fragment: Kinase Domain, Residues 598-899
Synonym: Ephb4 Receptor Tyrosine Kinase, Tyrosine-Protein Kinase 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 0.1655 R_Free 0.2090
crystal
cell
length a length b length c angle alpha angle beta angle gamma
45.777 53.451 61.347 90.00 110.57 90.00
method X-Ray Diffractionresolution 1.65 Å
ligand 7X4, MG BindingDB enzyme Transferase E.C.2.7.10.1 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceInhibitors of the tyrosine kinase EphB4. Part 2: Structure-based discovery and optimisation of 3,5-bis substituted anilinopyrimidines., Bardelle C, Coleman T, Cross D, Davenport S, Kettle JG, Ko EJ, Leach AG, Mortlock A, Read J, Roberts NJ, Robins P, Williams EJ, Bioorg Med Chem Lett. 2008 Sep 27. PMID:18851911
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (56 Kb) [Save to disk]
  • Biological Unit Coordinates (2vwx.pdb1.gz) 51 Kb
  • LPC: Ligand-Protein Contacts for 2VWX
  • CSU: Contacts of Structural Units for 2VWX
  • Likely Quarternary Molecular Structure file(s) for 2VWX
  • Structure Factors (373 Kb)
  • Retrieve 2VWX in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2VWX from S2C, [Save to disk]
  • Re-refined 2vwx structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2VWX 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 2VWX
  • 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 2VWX, from MSDmotif at EBI
  • Fold representative 2vwx from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2vwx] [2vwx_A]
  • SWISS-PROT database: [P54760]
  • Domain organization of [EPHB4_HUMAN] by SWISSPFAM
  • Domain found in 2VWX: [TyrKc ] by SMART
  • Alignments of the sequence of 2VWX with the sequences similar proteins can be viewed for 2VWX's classification [EPHB4_HUMAN] 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 [EPHB4_HUMAN] at ProtoMap. Click on the Cluster number.
  • Other resources with information on 2VWX
  • Community annotation for 2VWX 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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