3DKG	Oncoprotein	date	Jun 24, 2008
title	Sgx Clone 5698a109kfg1h1
authors	J.Hendle
compound		source
Molecule: Met Proto-Oncogene Chain: A Synonym: Hepatocyte Growth Factor Receptor, Met Proto- Oncogene (Hepatocyte Growth Factor Receptor), Isoform Cra_c; Engineered: Yes Mutation: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Gene: Met, Hcg_38705, Tcag7.66 Expression_system: Spodoptera Frugiperda Expression_system_common: Fall Armyworm Expression_system_taxid: 7108 Expression_system_cell_line: Sf9 Expression_system_vector_type: Baculovirus
symmetry	Space Group: P 21 21 21	R_factor 0.195 R_Free 0.238
crystal cell	length a length b length c angle alpha angle beta angle gamma 42.972 46.452 159.236 90.00 90.00 90.00
method	X-Ray Diffraction	resolution	1.91 Å
ligand	CL, SX8 BindingDB	enzyme
Gene	HCG
Primary reference	SGX523 is an exquisitely selective, ATP-competitive inhibitor of the MET receptor tyrosine kinase with antitumor activity in vivo., Buchanan SG, Hendle J, Lee PS, Smith CR, Bounaud PY, Jessen KA, Tang CM, Huser NH, Felce JD, Froning KJ, Peterman MC, Aubol BE, Gessert SF, Sauder JM, Schwinn KD, Russell M, Rooney IA, Adams J, Leon BC, Do TH, Blaney JM, Sprengeler PA, Thompson DA, Smyth L, Pelletier LA, Atwell S, Holme K, Wasserman SR, Emtage S, Burley SK, Reich SH, Mol Cancer Ther. 2009 Dec;8(12):3181-90. Epub . PMID:19934279

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (53 Kb) [Save to disk] Biological Unit Coordinates (3dkg.pdb1.gz) 49 Kb LPC: Ligand-Protein Contacts for 3DKG CSU: Contacts of Structural Units for 3DKG Likely Quarternary Molecular Structure file(s) for 3DKG Structure Factors (224 Kb) Retrieve 3DKG in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 3DKG from S2C, [Save to disk] Re-refined 3dkg structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 3DKG 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 3DKG

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 3DKG, from MSDmotif at EBI Fold representative 3dkg from FSSP and Dali (Families of Structurally Similar Proteins)

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [3dkg_A] SWISS-PROT database: [P08581] Domain organization of [MET_HUMAN] by SWISSPFAM Domain found in 3DKG: [TyrKc ] by SMART Alignments of the sequence of 3DKG with the sequences similar proteins can be viewed for 3DKG's classification [MET_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 [MET_HUMAN] at ProtoMap. Click on the Cluster number.

Other resources with information on 3DKG

Community annotation for 3DKG 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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