2GY5	Transferase	date	May 09, 2006
title	Tie2 Ligand-Binding Domain Crystal Structure
authors	W.A.Barton, D.B.Nikolov
compound		source
Molecule: Angiopoietin-1 Receptor Chain: A Fragment: Ligand-Binding Domain (Residues 23-445) Synonym: Tyrosine-Protein Kinase Receptor Tie-2, Htie2, Tyr Protein Kinase Receptor Tek, P140 Tek, Tunica Interna Endot Cell Kinase, Cd202b Antigen; Ec: 2.7.10.1 Engineered: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Expression_system: Cell Free Synthesis Expression_system_cell_line: Hek 293 Expression_system_vector: Pcdna3.1 (Invitrogen)
symmetry	Space Group: P 41 21 2	R_factor 0.240 R_Free 0.294
crystal cell	length a length b length c angle alpha angle beta angle gamma 114.653 114.653 113.774 90.00 90.00 90.00
method	X-Ray Diffraction	resolution	2.90 Å
ligand	NAG, NDG, SO4	enzyme	Transferase E.C.2.7.10.1 BRENDA
Primary reference	Crystal structures of the Tie2 receptor ectodomain and the angiopoietin-2-Tie2 complex., Barton WA, Tzvetkova-Robev D, Miranda EP, Kolev MV, Rajashankar KR, Himanen JP, Nikolov DB, Nat Struct Mol Biol. 2006 Jun;13(6):524-532. Epub 2006 May 28. PMID:16732286

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (75 Kb) [Save to disk] Biological Unit Coordinates (2gy5.pdb1.gz) 70 Kb LPC: Ligand-Protein Contacts for 2GY5 CSU: Contacts of Structural Units for 2GY5 Likely Quarternary Molecular Structure file(s) for 2GY5 Structure Factors (634 Kb) Retrieve 2GY5 in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 2GY5 from S2C, [Save to disk] Re-refined 2gy5 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 2GY5 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 2GY5

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 2GY5, from MSDmotif at EBI Fold representative 2gy5 from FSSP and Dali (Families of Structurally Similar Proteins)

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [2gy5_A] SWISS-PROT database: [Q02763] Domain organization of [TIE2_HUMAN] by SWISSPFAM Domains found in 2GY5: [EGF] [EGF_like] [IG_like ] by SMART Alignments of the sequence of 2GY5 with the sequences similar proteins can be viewed for 2GY5's classification [TIE2_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 [TIE2_HUMAN] at ProtoMap. Click on the Cluster number.

Other resources with information on 2GY5

Community annotation for 2GY5 at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

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