1VFY: PDB entry 1VFY

Phosphatidylinositol-3-phosphate binding fyve domain of VPS27P protein from saccharomyces cerevisiae. Determined by X-ray diffraction at 1.15 Å resolution. Released 6 May 1999.

Method: X-ray diffraction
Resolution: 1.15 Å
Organism: Saccharomyces cerevisiae
Chains: 1
Atoms: 643
Mol. weight: 8.4 kDa
Ligands: ZN
Released: 6 May 1999

Explore 1VFY in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1VFY contains 5 α-helices and 8 β-strands across 1 chain. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 5 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	175	1	1
α-helix	181	1
β-strand	182	1	1
α-helix	183	1
β-strand	184	1	2
β-strand	187	1	2
β-strand	190-191	2	3
β-strand	198-199	2	3
α-helix	201-203	3
β-strand	206-210	5	4
α-helix	211-213	3
β-strand	215-221	7	4
α-helix	223-234	12

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Phosphatidylinositol-3-phosphate binding fyve domain of protein VPS27	A	protein	73	Saccharomyces cerevisiae	P40343 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>1VFY_1 PHOSPHATIDYLINOSITOL-3-PHOSPHATE BINDING FYVE DOMAIN OF PROTEIN VPS27 (chains A)
DSKTPADWIDSDACMICSKKFSLLNRKHHCRSCGGVFCQEHSSNSIPLPDLGIYEPVRVC
DSCFEDYEFIVTD

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	2

Primary citation

Crystal structure of a phosphatidylinositol 3-phosphate-specific membrane-targeting motif, the FYVE domain of Vps27p. Misra, S., Hurley, J.H. Cell (1999) 97:657-666. DOI 10.1016/S0092-8674(00)80776-X · PubMed

Other PDB entries of the same protein (UniProt P40343 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1O06 1.45 Å, Crystal structure of the Vps27p Ubiquitin Interacting Motif (UIM)
3R42 1.87 Å, Crystal structure of the yeast vps23 UEV domain in complex with a vps27 PSDP peptide
6NJG 2.35 Å, Ubiquitin Variant in Complex with Ubiquitin Interacting Motif
2PJW 3.01 Å, The Vps27/Hse1 complex is a GAT domain-based scaffold for ubiquitin-dependent sorting
1Q0V Solution Structure of Tandem UIMs of Vps27
1Q0W Solution structure of Vps27 amino-terminal UIM-ubiquitin complex
2KDI Solution structure of a Ubiquitin/UIM fusion protein

Browse structure collections

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