2VWY	Transferase	date	Jun 30, 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 0.18736 R_Free 0.23805
crystal cell	length a length b length c angle alpha angle beta angle gamma 46.073 53.479 61.517 90.00 110.90 90.00
method	X-Ray Diffraction	resolution	1.65 Å
ligand	7X5, MG BindingDB	enzyme	Transferase E.C.2.7.10.1 BRENDA
Primary reference	Inhibitors 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 (2vwy.pdb1.gz) 50 Kb LPC: Ligand-Protein Contacts for 2VWY CSU: Contacts of Structural Units for 2VWY Likely Quarternary Molecular Structure file(s) for 2VWY Structure Factors (220 Kb) Retrieve 2VWY in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 2VWY from S2C, [Save to disk] Re-refined 2vwy structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 2VWY 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. On AstexViewer, from MSD-EBI (viewer documentation). On RasMol (Install RasMol freeware) Here's help on how to use RasMol.

Visual 3D analysis of 2VWY

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 2VWY, from MSDmotif at EBI Fold representative 2vwy from FSSP and Dali (Families of Structurally Similar Proteins)

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [2vwy_A] SWISS-PROT database: [P54760] Domain organization of [EPHB4_HUMAN] by SWISSPFAM Domain found in 2VWY: [TyrKc ] by SMART Alignments of the sequence of 2VWY with the sequences similar proteins can be viewed for 2VWY'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 2VWY

Community annotation for 2VWY at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

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