Annotations: 6NDY

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	ubiquitin	e6ndyA1	A: a/b three-layered sandwiches	X: Ten stranded beta/alpha barrel	H: Ten stranded beta/alpha barrel	T: Ten stranded beta/alpha barrel	F: ubiquitin	ECOD (v294.1)
C	ubiquitin	e6ndyC1	A: a/b three-layered sandwiches	X: Ten stranded beta/alpha barrel	H: Ten stranded beta/alpha barrel	T: Ten stranded beta/alpha barrel	F: ubiquitin	ECOD (v294.1)
D	ubiquitin	e6ndyD1	A: a/b three-layered sandwiches	X: Ten stranded beta/alpha barrel	H: Ten stranded beta/alpha barrel	T: Ten stranded beta/alpha barrel	F: ubiquitin	ECOD (v294.1)
E	ubiquitin	e6ndyE1	A: a/b three-layered sandwiches	X: Ten stranded beta/alpha barrel	H: Ten stranded beta/alpha barrel	T: Ten stranded beta/alpha barrel	F: ubiquitin	ECOD (v294.1)
B	ubiquitin	e6ndyB1	A: a/b three-layered sandwiches	X: Ten stranded beta/alpha barrel	H: Ten stranded beta/alpha barrel	T: Ten stranded beta/alpha barrel	F: ubiquitin	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (utative)
A	1.10.8.60	Mainly Alpha	Orthogonal Bundle	Helicase, Ruva Protein	domain 3	CATH (utative)
C	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (utative)
C	1.10.8.60	Mainly Alpha	Orthogonal Bundle	Helicase, Ruva Protein	domain 3	CATH (utative)
D	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (utative)
D	1.10.8.60	Mainly Alpha	Orthogonal Bundle	Helicase, Ruva Protein	domain 3	CATH (utative)
E	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (utative)
E	1.10.8.60	Mainly Alpha	Orthogonal Bundle	Helicase, Ruva Protein	domain 3	CATH (utative)
B	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (utative)
B	1.10.8.60	Mainly Alpha	Orthogonal Bundle	Helicase, Ruva Protein	domain 3	CATH (utative)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D, E	PF09336	Vps4 C terminal oligomerisation domain (Vps4_C)	Vps4 C terminal oligomerisation domain	This domain is found at the C terminal of ATPase proteins involved in vacuolar sorting. It forms an alpha helix structure and is required for oligomerisation [1].	Domain
A, B, C, D, E	PF17862	AAA+ lid domain (AAA_lid_3)	AAA+ lid domain	This entry represents the alpha helical AAA+ lid domain that is found to the C-terminus of AAA domains.	Domain
A, B, C, D, E	PF00004	ATPase family associated with various cellular activities (AAA) (AAA)	ATPase family associated with various cellular activities (AAA)	AAA family proteins often perform chaperone-like functions that assist in the assembly, operation, or disassembly of protein complexes [2].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
F [auth G]	Designed Cyclic Peptide	-	-	-
A, B, C, D, E	Vacuolar protein sorting-associated protein 4	binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding identical protein binding protein binding protein homodimerization activity protein dimerization activity pyrophosphatase activity ATP hydrolysis activity ribonucleoside triphosphate phosphatase activity hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides hydrolase activity hydrolase activity, acting on acid anhydrides catalytic activity ATP-dependent activity	localization cellular localization late endosome to vacuole transport transport establishment of localization in cell cellular process vacuolar transport intracellular transport establishment of localization vesicle-mediated transport endosomal transport late endosome to vacuole transport via multivesicular body sorting pathway multivesicular body sorting pathway endosome transport via multivesicular body sorting pathway localization cellular localization late endosome to vacuole transport transport establishment of localization in cell cellular process vacuolar transport intracellular transport establishment of localization vesicle-mediated transport endosomal transport late endosome to vacuole transport via multivesicular body sorting pathway multivesicular body sorting pathway endosome transport via multivesicular body sorting pathway cellular component disassembly catabolic process protein-containing complex organization macroautophagy autophagy protein-containing complex disassembly cellular component organization autophagosome maturation metabolic process cellular component organization or biogenesis process utilizing autophagic mechanism membrane organization membrane biogenesis nuclear membrane reassembly membrane assembly nuclear membrane organization cellular component biogenesis nucleus organization organelle organization cellular component assembly nuclear envelope organization endomembrane system organization sterol metabolic process steroid metabolic process primary metabolic process lipid metabolic process late endosome to lysosome transport endosome to lysosome transport lysosomal transport endosome to lysosome transport via multivesicular body sorting pathway late endosome to lysosome transport via multivesicular body sorting pathway organelle assembly multivesicular body assembly vesicle organization multivesicular body organization endosome organization establishment of protein localization protein transport macromolecule localization intracellular protein localization protein catabolic process macromolecule catabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway ubiquitin-dependent protein catabolic process protein metabolic process macromolecule metabolic process cytoskeleton-dependent cytokinesis mitotic cytokinetic process mitotic cytokinesis cytokinesis mitotic cell cycle mitotic cell cycle process midbody abscission cytokinetic process cell cycle cell division cell cycle process ubiquitin-independent protein catabolic process via the multivesicular body sorting pathway membrane fission maintenance of protein location protein localization to Golgi apparatus maintenance of location maintenance of location in cell maintenance of protein location in cell protein localization to organelle protein retention in Golgi apparatus vesicle budding from membrane intralumenal vesicle formation wound healing response to stimulus plasma membrane repair response to stress plasma membrane organization response to wounding vacuole organization reticulophagy	midbody cellular anatomical structure membrane-bounded organelle endosome membrane protein-containing complex ATPase complex intracellular anatomical structure intracellular vesicle membrane protein complex endomembrane system intracellular organelle bounding membrane of organelle cytoplasmic vesicle vesicle membrane midbody cellular anatomical structure membrane-bounded organelle endosome membrane protein-containing complex ATPase complex intracellular anatomical structure intracellular vesicle membrane protein complex endomembrane system intracellular organelle bounding membrane of organelle cytoplasmic vesicle vesicle membrane vesicle catalytic complex ESCRT complex endosome membrane intracellular membrane-bounded organelle cytoplasmic vesicle membrane organelle ESCRT IV complex cytoplasm organelle membrane cell periphery plasma membrane nucleus nuclear protein-containing complex organelle envelope nuclear envelope nuclear pore endoplasmic reticulum

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E	IPR003593	AAA+ ATPase domain	Domain
A, B, C, D, E	IPR003959	ATPase, AAA-type, core	Domain
A, B, C, D, E	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
A, B, C, D, E	IPR007330	MIT domain	Domain
A, B, C, D, E	IPR041569	AAA ATPase, AAA+ lid domain	Domain
A, B, C, D, E	IPR015415	Spastin/Vps4, C-terminal	Domain
A, B, C, D, E	IPR050304	Microtubule-severing AAA ATPase	Family
A, B, C, D, E	IPR045253	Vacuolar protein sorting-associated protein 4, MIT domain	Domain
A, B, C, D, E	IPR003960	ATPase, AAA-type, conserved site	Conserved Site
A, B, C, D, E	IPR036181	MIT domain superfamily	Homologous Superfamily

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.