6XS9 | pdb_00006xs9

Crystal structure of human Vps29 complexed with RaPID-derived cyclic peptide RT-L1

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations
Protein Modification Annotation

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2B Superfamily	Metallo-dependent phosphatases	8036532	3001067	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Metallo-dependent phosphatases	8036532	3001067	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
B	Trypsin	e6xs9B1	A: alpha bundles	X: CNF1/YfiH-like putative cysteine hydrolases	H: RIFT-related	T: FMN-binding split barrel 2	F: Trypsin	ECOD (develop294)
A	Lys	e6xs9A1	A: alpha bundles	X: CNF1/YfiH-like putative cysteine hydrolases	H: Bromodomain	T: Bromodomain	F: Lys	ECOD (develop294)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B	PF12850	Calcineurin-like phosphoesterase superfamily domain (Metallophos_2)	Calcineurin-like phosphoesterase superfamily domain	Members of this family are part of the Calcineurin-like phosphoesterase superfamily.	Domain
A	PF12850	Calcineurin-like phosphoesterase superfamily domain (Metallophos_2)	Calcineurin-like phosphoesterase superfamily domain	Members of this family are part of the Calcineurin-like phosphoesterase superfamily.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
C, D, E, F	48V-TYR-ILE-LYS-THR-PRO-LEU-GLY-THR-PHE-PRO-ASN-ARG-HIS-GLY	-	-	-
B	Vacuolar protein sorting-associated protein 29	cation binding ion binding binding metal ion binding small molecule binding	cellular localization establishment of protein localization transport intracellular transport establishment of localization localization protein transport establishment of localization in cell macromolecule localization cellular process intracellular protein localization intracellular protein transport vesicle-mediated transport endosomal transport cellular localization establishment of protein localization transport intracellular transport establishment of localization localization protein transport establishment of localization in cell macromolecule localization cellular process intracellular protein localization intracellular protein transport vesicle-mediated transport endosomal transport cytosolic transport retrograde transport, endosome to Golgi localization within membrane endocytic recycling vesicle-mediated transport to the plasma membrane	membrane-bounded organelle intracellular anatomical structure early endosome endosome intracellular vesicle intracellular membrane-bounded organelle endomembrane system intracellular organelle cellular anatomical structure cytoplasmic vesicle organelle cytoplasm vesicle protein-containing complex membrane-bounded organelle intracellular anatomical structure early endosome endosome intracellular vesicle intracellular membrane-bounded organelle endomembrane system intracellular organelle cellular anatomical structure cytoplasmic vesicle organelle cytoplasm vesicle protein-containing complex membrane membrane protein complex retromer complex retromer, cargo-selective complex cytosol endosome membrane cytoplasmic vesicle membrane bounding membrane of organelle vesicle membrane organelle membrane late endosome
A	Vacuolar protein sorting-associated protein 29	cation binding ion binding binding metal ion binding small molecule binding	cellular localization establishment of protein localization transport intracellular transport establishment of localization localization protein transport establishment of localization in cell macromolecule localization cellular process intracellular protein localization intracellular protein transport vesicle-mediated transport endosomal transport cellular localization establishment of protein localization transport intracellular transport establishment of localization localization protein transport establishment of localization in cell macromolecule localization cellular process intracellular protein localization intracellular protein transport vesicle-mediated transport endosomal transport cytosolic transport retrograde transport, endosome to Golgi localization within membrane endocytic recycling vesicle-mediated transport to the plasma membrane	membrane-bounded organelle intracellular anatomical structure early endosome endosome intracellular vesicle intracellular membrane-bounded organelle endomembrane system intracellular organelle cellular anatomical structure cytoplasmic vesicle organelle cytoplasm vesicle protein-containing complex membrane-bounded organelle intracellular anatomical structure early endosome endosome intracellular vesicle intracellular membrane-bounded organelle endomembrane system intracellular organelle cellular anatomical structure cytoplasmic vesicle organelle cytoplasm vesicle protein-containing complex membrane membrane protein complex retromer complex retromer, cargo-selective complex cytosol endosome membrane cytoplasmic vesicle membrane bounding membrane of organelle vesicle membrane organelle membrane late endosome

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B	IPR000979	Phosphodiesterase MJ0936/Vps29	Family
B	IPR024654	Calcineurin-like phosphoesterase domain, lpxH-type	Domain
B	IPR029052	Metallo-dependent phosphatase-like	Homologous Superfamily
B	IPR028661	Vacuolar protein sorting-associated protein 29	Family
A	IPR000979	Phosphodiesterase MJ0936/Vps29	Family
A	IPR024654	Calcineurin-like phosphoesterase domain, lpxH-type	Domain
A	IPR029052	Metallo-dependent phosphatase-like	Homologous Superfamily
A	IPR028661	Vacuolar protein sorting-associated protein 29	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
B	Pharos: Q9UBQ0	breast carcinoma ovarian cancer hereditary spastic paraplegia pancreatic ductal adenocarcinoma malignant pancreatic neoplasm
A	Pharos: Q9UBQ0	breast carcinoma ovarian cancer hereditary spastic paraplegia pancreatic ductal adenocarcinoma malignant pancreatic neoplasm

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
C, D, E, F	48V
B	CSO	Parent Component: CYS RESID: AA0205 PSI-MOD : L-cysteine sulfenic acid MOD:00210

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.

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