3VQI | pdb_00003vqi

Crystal structure of Kluyveromyces marxianus Atg5

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	ATG5-like	8045343	4004425	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Ubiquitin-like	8084654	3000157	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Ubiquitin-like	8090300	3000157	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	Ubiquitin-like	8084654	3000157	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Ubiquitin-like	8090300	3000157	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Ubiquitin-like	8084654	3000157	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Ubiquitin-like	8090300	3000157	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Ubiquitin-like	8084654	3000157	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Ubiquitin-like	8090300	3000157	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Ubiquitin-like	8090300	3000157	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Ubiquitin-like	8084654	3000157	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)
A	APG5_1st	e3vqiA6	A: alpha bundles	X: Helical domain in autophagy protein 5 (From Topology)	H: Helical domain in autophagy protein 5 (From Topology)	T: Helical domain in autophagy protein 5	F: APG5_1st	ECOD (1.6)
A	APG5_2nd	e3vqiA7	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: APG5_2nd	ECOD (1.6)
A	KOG2976	e3vqiA2	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: KOG2976	ECOD (1.6)
B	APG5_1st	e3vqiB10	A: alpha bundles	X: Helical domain in autophagy protein 5 (From Topology)	H: Helical domain in autophagy protein 5 (From Topology)	T: Helical domain in autophagy protein 5	F: APG5_1st	ECOD (1.6)
B	APG5_2nd	e3vqiB12	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: APG5_2nd	ECOD (1.6)
B	KOG2976	e3vqiB11	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: KOG2976	ECOD (1.6)
C	APG5_1st	e3vqiC10	A: alpha bundles	X: Helical domain in autophagy protein 5 (From Topology)	H: Helical domain in autophagy protein 5 (From Topology)	T: Helical domain in autophagy protein 5	F: APG5_1st	ECOD (1.6)
C	APG5_2nd	e3vqiC12	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: APG5_2nd	ECOD (1.6)
C	KOG2976	e3vqiC11	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: KOG2976	ECOD (1.6)
D	APG5_1st	e3vqiD10	A: alpha bundles	X: Helical domain in autophagy protein 5 (From Topology)	H: Helical domain in autophagy protein 5 (From Topology)	T: Helical domain in autophagy protein 5	F: APG5_1st	ECOD (1.6)
D	APG5_2nd	e3vqiD12	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: APG5_2nd	ECOD (1.6)
D	KOG2976	e3vqiD11	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: KOG2976	ECOD (1.6)
E	APG5_1st	e3vqiE10	A: alpha bundles	X: Helical domain in autophagy protein 5 (From Topology)	H: Helical domain in autophagy protein 5 (From Topology)	T: Helical domain in autophagy protein 5	F: APG5_1st	ECOD (1.6)
E	APG5_2nd	e3vqiE12	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: APG5_2nd	ECOD (1.6)
E	KOG2976	e3vqiE11	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: KOG2976	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.10.20.620	Alpha Beta	Roll	Ubiquitin-like (UB roll)		CATH (4.3.0)
A	1.10.246.190	Mainly Alpha	Orthogonal Bundle	Serum Albumin	Chain A, Domain 1	CATH (4.3.0)
A	3.10.20.90	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Phosphatidylinositol 3-kinase Catalytic Subunit	CATH (4.3.0)
B	3.10.20.620	Alpha Beta	Roll	Ubiquitin-like (UB roll)		CATH (4.3.0)
B	1.10.246.190	Mainly Alpha	Orthogonal Bundle	Serum Albumin	Chain A, Domain 1	CATH (4.3.0)
B	3.10.20.90	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Phosphatidylinositol 3-kinase Catalytic Subunit	CATH (4.3.0)
C	3.10.20.620	Alpha Beta	Roll	Ubiquitin-like (UB roll)		CATH (4.3.0)
C	1.10.246.190	Mainly Alpha	Orthogonal Bundle	Serum Albumin	Chain A, Domain 1	CATH (4.3.0)
C	3.10.20.90	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Phosphatidylinositol 3-kinase Catalytic Subunit	CATH (4.3.0)
D	3.10.20.620	Alpha Beta	Roll	Ubiquitin-like (UB roll)		CATH (4.3.0)
D	1.10.246.190	Mainly Alpha	Orthogonal Bundle	Serum Albumin	Chain A, Domain 1	CATH (4.3.0)
D	3.10.20.90	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Phosphatidylinositol 3-kinase Catalytic Subunit	CATH (4.3.0)
E	3.10.20.620	Alpha Beta	Roll	Ubiquitin-like (UB roll)		CATH (4.3.0)
E	1.10.246.190	Mainly Alpha	Orthogonal Bundle	Serum Albumin	Chain A, Domain 1	CATH (4.3.0)
E	3.10.20.90	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Phosphatidylinositol 3-kinase Catalytic Subunit	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D, E	PF20637	Autophagy protein ATG5, alpha-helical bundle region (ATG5_HBR)	Autophagy protein ATG5, alpha-helical bundle region	Autophagy protein ATG5 is involved in autophagic vesicle formation. It is conjugated with ATG12, acting as an E3-like ubiquitin enzyme required for lipidation of ATG8 family proteins and their association to the vesicle membranes. ATG5 comprises two ...	Autophagy protein ATG5 is involved in autophagic vesicle formation. It is conjugated with ATG12, acting as an E3-like ubiquitin enzyme required for lipidation of ATG8 family proteins and their association to the vesicle membranes. ATG5 comprises two ubiquitin-like domains (UblA and UblB) that flank a helix-rich domain. This domain represents the alpha-helical bundle region (HBR) of AT5 which consists of three alpha helices [1,2]. This region contains the Lys residue required for conjugation with ATG12 [1].	Domain
A, B, C, D, E	PF20638	Autophagy protein ATG5, UblA domain (ATG5_UblA)	Autophagy protein ATG5, UblA domain	This is the N-terminal ubiquitin-like domain, termed UblA, from autophagy protein ATG5 [1,2]. ATG5 comprises two ubiquitin-like domains (UblA and UblB) that flank a helix-rich domain (HBR). Both UblA and UblB comprise a five-stranded sheet and two-he ...	This is the N-terminal ubiquitin-like domain, termed UblA, from autophagy protein ATG5 [1,2]. ATG5 comprises two ubiquitin-like domains (UblA and UblB) that flank a helix-rich domain (HBR). Both UblA and UblB comprise a five-stranded sheet and two-helices.	Domain
A, B, C, D, E	PF04106	Autophagy protein ATG5, UblB domain (ATG5_UblB)	Autophagy protein ATG5, UblB domain	ATG5 is directly required for the import of aminopeptidase I via the cytoplasm-to-vacuole targeting pathway [1]. ATG5 is conjugated to ATG12; this conjugate exhibits E3 ligase-like activity which facilitates the lipidation of members of the LC3 famil ...	ATG5 is directly required for the import of aminopeptidase I via the cytoplasm-to-vacuole targeting pathway [1]. ATG5 is conjugated to ATG12; this conjugate exhibits E3 ligase-like activity which facilitates the lipidation of members of the LC3 family, and therefore autophagosome formation [2]. ATG5 comprises N- and C-terminal ubiquitin-like domains (UblA and UblB) that flank the helical-rich region (HBR). This is the UblB domain, found at the C-terminal [2,3].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D, E	Atg5	aminoacyltransferase activity ubiquitin-like protein transferase activity catalytic activity, acting on a protein acyltransferase activity Atg8-family ligase activity ubiquitin-like protein ligase activity transferase activity catalytic activity	catabolic process autophagy cellular process metabolic process autophagy of mitochondrion process utilizing autophagic mechanism cellular response to stimulus response to nutrient levels cellular response to nitrogen levels response to stimulus cellular response to starvation cellular response to nutrient levels cellular response to stress cellular response to nitrogen starvation catabolic process autophagy cellular process metabolic process autophagy of mitochondrion process utilizing autophagic mechanism cellular response to stimulus response to nutrient levels cellular response to nitrogen levels response to stimulus cellular response to starvation cellular response to nutrient levels cellular response to stress cellular response to nitrogen starvation response to stress response to starvation macroautophagy piecemeal microautophagy of the nucleus microautophagy nucleophagy protein localization establishment of protein localization cellular localization nitrogen compound transport transport establishment of localization localization protein transport cellular macromolecule localization macromolecule localization	organelle membrane contact site cellular anatomical structure organelle mitochondria-associated endoplasmic reticulum membrane contact site protein-containing complex intracellular anatomical structure catalytic complex Atg12-Atg5-Atg16 complex transferase complex cytoplasm membrane-bounded organelle intracellular organelle vacuole autophagosome organelle membrane contact site cellular anatomical structure organelle mitochondria-associated endoplasmic reticulum membrane contact site protein-containing complex intracellular anatomical structure catalytic complex Atg12-Atg5-Atg16 complex transferase complex cytoplasm membrane-bounded organelle intracellular organelle vacuole autophagosome intracellular membrane-bounded organelle phagophore phagophore assembly site membrane membrane phagophore assembly site

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E	IPR042527	Autophagy protein Atg5, UblA domain superfamily	Homologous Superfamily
A, B, C, D, E	IPR048940	Autophagy protein ATG5, alpha-helical bundle region	Domain
A, B, C, D, E	IPR042526	Autophagy protein Atg5, helix rich domain	Homologous Superfamily
A, B, C, D, E	IPR048318	Autophagy protein ATG5, UblB domain	Domain
A, B, C, D, E	IPR048939	Autophagy protein ATG5, UblA domain	Domain
A, B, C, D, E	IPR007239	Autophagy-related protein 5	Family

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.