1VFY Transport Protein date Apr 26, 1999
title Phosphatidylinositol-3-Phosphate Binding Fyve Domain Of Vps2 From Saccharomyces Cerevisiae
authors J.H.Hurley, S.Misra
compound source
Molecule: Phosphatidylinositol-3-Phosphate Binding Fyve Dom Protein Vps27;
Chain: A
Fragment: 163-229, Fyve Domain
Engineered: Yes
Mutation: Yes
Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932
Cellular_location: Cytoplasm, Endosomal Membranes
Gene: Vps27
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21
Expression_system_variant: De3
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pgex-2t
symmetry Space Group: P 1
R_factor 0.174 R_Free 0.181
crystal
cell
length a length b length c angle alpha angle beta angle gamma
24.090 26.570 31.610 111.79 92.70 105.70
method X-Ray Diffractionresolution 1.15 Å
ligand ZN enzyme
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceCrystal structure of a phosphatidylinositol 3-phosphate-specific membrane-targeting motif, the FYVE domain of Vps27p., Misra S, Hurley JH, Cell 1999 May 28;97(5):657-66. PMID:10367894
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (18 Kb) [Save to disk]
  • Biological Unit Coordinates (1vfy.pdb1.gz) 13 Kb
  • LPC: Ligand-Protein Contacts for 1VFY
  • CSU: Contacts of Structural Units for 1VFY
  • Likely Quarternary Molecular Structure file(s) for 1VFY
  • Structure Factors (147 Kb)
  • Retrieve 1VFY in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1VFY from S2C, [Save to disk]
  • Re-refined 1vfy structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1VFY 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 1VFY
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Conformational Epitope Prediction for 1VFY from the CEP Server.
  • Electron Density related parameters from EDS Electron Density Server, at Upsala
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 1VFY, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1vfya_, region A [Jmol] [rasmolscript] [script source]
  • Class (fold), Architecture (subfold), Topology, Homologous superfamily from CATH
  • Summaries and structural analyses of PDB data files from PDBSum
  • Identification of Protein Pockets & Cavities at CASTp
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1vfy] [1vfy_A]
  • SWISS-PROT database: [P40343]
  • Domain organization of [VPS27_YEAST] by SWISSPFAM
  • Domain found in 1VFY: [FYVE ] by SMART
  • Other resources with information on 1VFY
  • Community annotation for 1VFY 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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