3KYQ	Transferase	date	Dec 07, 2009
title	Lipid-Induced Conformational Switch Controls Fusion Activity Domain Snare Ykt6
authors	J.Yu, W.Y.Wen, M.J.Zhang
compound		source
Molecule: Synaptobrevin Homolog Ykt6 Chain: A Synonym: Ykt6 Ec: 2.3.1.- Engineered: Yes		Organism_scientific: Rattus Norvegicus Organism_common: Rat Organism_taxid: 10116 Gene: Ykt6 Expression_system: Escherichia Coli Expression_system_taxid: 469008 Expression_system_strain: Bl21 De3 Expression_system_vector_type: Plasmid Expression_system_plasmid: Modified Pet32a
symmetry	Space Group: C 2 2 21	R_factor 0.199 R_Free 0.261
crystal cell	length a length b length c angle alpha angle beta angle gamma 54.810 59.710 108.330 90.00 90.00 90.00
method	X-Ray Diffraction	resolution	2.44 Å
ligand	DPV, SO4	enzyme	Transferase E.C.2.3.1 BRENDA
Gene Ontology	Chain Function Process Component A SNAP receptor activity
Primary reference	Lipid-Induced conformational switch controls fusion activity of longin domain SNARE Ykt6., Wen W, Yu J, Pan L, Wei Z, Weng J, Wang W, Ong YS, Tran TH, Hong W, Zhang M, Mol Cell. 2010 Feb 12;37(3):383-95. PMID:20159557

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (38 Kb) [Save to disk] Biological Unit Coordinates (3kyq.pdb1.gz) 33 Kb LPC: Ligand-Protein Contacts for 3KYQ CSU: Contacts of Structural Units for 3KYQ Structure Factors (340 Kb) Retrieve 3KYQ in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 3KYQ from S2C, [Save to disk] Re-refined 3kyq structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 3KYQ 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 3KYQ

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 3D motif for 3KYQ, from MSDmotif at EBI

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [3kyq] [3kyq_A] SWISS-PROT database: Domain organization of by SWISSPFAM Domain found in 3KYQ: [Longin ] by SMART

Other resources with information on 3KYQ

Community annotation for 3KYQ at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

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