7VEC | pdb_00007vec

Crystal structure of GABARAP complexed with the TEX264 LIR phosphorylated at Ser271 and Ser272

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
Pharos: Disease Associations
Protein Modification Annotation

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
L	SCOP2B Superfamily	Ubiquitin-like	8040431	3000157	SCOP2B (2022-06-29)
K	SCOP2B Superfamily	Ubiquitin-like	8040431	3000157	SCOP2B (2022-06-29)
J	SCOP2B Superfamily	Ubiquitin-like	8040431	3000157	SCOP2B (2022-06-29)
I	SCOP2B Superfamily	Ubiquitin-like	8040431	3000157	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	Ubiquitin-like	8040431	3000157	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	Ubiquitin-like	8040431	3000157	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Ubiquitin-like	8040431	3000157	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Ubiquitin-like	8040431	3000157	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Ubiquitin-like	8040431	3000157	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Ubiquitin-like	8040431	3000157	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Ubiquitin-like	8040431	3000157	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Ubiquitin-like	8040431	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)
L	Peptidase_C30	e7vecL1	A: beta barrels	X: Nuclear receptor ligand-binding domain	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Peptidase_C30	ECOD (v294.2)
K	Peptidase_C30	e7vecK1	A: beta barrels	X: Nuclear receptor ligand-binding domain	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Peptidase_C30	ECOD (v294.2)
J	Peptidase_C30	e7vecJ1	A: beta barrels	X: Nuclear receptor ligand-binding domain	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Peptidase_C30	ECOD (v294.2)
I	Peptidase_C30	e7vecI1	A: beta barrels	X: Nuclear receptor ligand-binding domain	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Peptidase_C30	ECOD (v294.2)
H	Peptidase_C30	e7vecH1	A: beta barrels	X: Nuclear receptor ligand-binding domain	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Peptidase_C30	ECOD (v294.2)
G	Peptidase_C30	e7vecG1	A: beta barrels	X: Nuclear receptor ligand-binding domain	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Peptidase_C30	ECOD (v294.2)
F	Peptidase_C30	e7vecF1	A: beta barrels	X: Nuclear receptor ligand-binding domain	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Peptidase_C30	ECOD (v294.2)
E	Peptidase_C30	e7vecE1	A: beta barrels	X: Nuclear receptor ligand-binding domain	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Peptidase_C30	ECOD (v294.2)
D	Peptidase_C30	e7vecD1	A: beta barrels	X: Nuclear receptor ligand-binding domain	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Peptidase_C30	ECOD (v294.2)
C	Peptidase_C30	e7vecC1	A: beta barrels	X: Nuclear receptor ligand-binding domain	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Peptidase_C30	ECOD (v294.2)
B	Peptidase_C30	e7vecB1	A: beta barrels	X: Nuclear receptor ligand-binding domain	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Peptidase_C30	ECOD (v294.2)
A	Peptidase_C30	e7vecA1	A: beta barrels	X: Nuclear receptor ligand-binding domain	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Peptidase_C30	ECOD (v294.2)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
L	3.10.20.90	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Phosphatidylinositol 3-kinase Catalytic Subunit	CATH (utative)
K	3.10.20.90	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Phosphatidylinositol 3-kinase Catalytic Subunit	CATH (utative)
J	3.10.20.90	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Phosphatidylinositol 3-kinase Catalytic Subunit	CATH (utative)
I	3.10.20.90	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Phosphatidylinositol 3-kinase Catalytic Subunit	CATH (utative)
H	3.10.20.90	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Phosphatidylinositol 3-kinase Catalytic Subunit	CATH (utative)
G	3.10.20.90	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Phosphatidylinositol 3-kinase Catalytic Subunit	CATH (utative)
F	3.10.20.90	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Phosphatidylinositol 3-kinase Catalytic Subunit	CATH (utative)
E	3.10.20.90	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Phosphatidylinositol 3-kinase Catalytic Subunit	CATH (utative)
D	3.10.20.90	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Phosphatidylinositol 3-kinase Catalytic Subunit	CATH (utative)
C	3.10.20.90	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Phosphatidylinositol 3-kinase Catalytic Subunit	CATH (utative)
B	3.10.20.90	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Phosphatidylinositol 3-kinase Catalytic Subunit	CATH (utative)
A	3.10.20.90	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Phosphatidylinositol 3-kinase Catalytic Subunit	CATH (utative)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	PF02991	Autophagy protein Atg8 ubiquitin like (ATG8)	Autophagy protein Atg8 ubiquitin like	Light chain 3 is proposed to function primarily as a subunit of microtubule associated proteins 1A and 1B and that its expression may regulate microtubule binding activity [1]. Autophagy is generally known as a process involved in the degradation of ...	Light chain 3 is proposed to function primarily as a subunit of microtubule associated proteins 1A and 1B and that its expression may regulate microtubule binding activity [1]. Autophagy is generally known as a process involved in the degradation of bulk cytoplasmic components that are non-specifically sequestered into an autophagosome, where they are sequestered into double-membrane vesicles and delivered to the degradative organelle, the lysosome/vacuole, for breakdown and eventual recycling of the resulting macromolecules. The yeast proteins are involved in the autophagosome, and Atg8 binds Atg19, via its N-terminus and the C-terminus of Atg19.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
M, N, O, P, Q, M, N, O, P, Q, R, S, T, U, V, W [auth X]	TEX264 phospho-LIR	molecular transducer activity signaling receptor activity	cellular response to stimulus response to stimulus primary metabolic process DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process cellular response to stress DNA damage response response to stress protein-DNA covalent cross-linking repair metabolic process cellular process macromolecule metabolic process DNA repair cellular response to stimulus response to stimulus primary metabolic process DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process cellular response to stress DNA damage response response to stress protein-DNA covalent cross-linking repair metabolic process cellular process macromolecule metabolic process DNA repair catabolic process macroautophagy reticulophagy autophagy process utilizing autophagic mechanism	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle vesicle lumen intracellular vesicle membrane-enclosed lumen cytoplasmic vesicle lumen intracellular membrane-bounded organelle secretory granule lumen endomembrane system intracellular organelle lumen intracellular organelle cellular anatomical structure intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle vesicle lumen intracellular vesicle membrane-enclosed lumen cytoplasmic vesicle lumen intracellular membrane-bounded organelle secretory granule lumen endomembrane system intracellular organelle lumen intracellular organelle cytoplasmic vesicle organelle lumen organelle secretory granule secretory vesicle platelet alpha granule vesicle platelet alpha granule lumen vacuolar membrane autophagosome membrane membrane vacuole autophagosome bounding membrane of organelle organelle membrane extracellular region membraneless organelle replication fork intracellular membraneless organelle chromosome nucleus endoplasmic reticulum organelle subcompartment endoplasmic reticulum subcompartment nuclear outer membrane-endoplasmic reticulum membrane network endoplasmic reticulum membrane
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	Gamma-aminobutyric acid receptor-associated protein	protein binding binding signaling receptor binding GABA receptor binding phosphatidylethanolamine binding phospholipid binding lipid binding cytoskeletal protein binding microtubule binding tubulin binding ubiquitin protein ligase binding ubiquitin-like protein ligase binding enzyme binding beta-tubulin binding	cellular response to stimulus regulation of biological process regulation of signaling small GTPase-mediated signal transduction regulation of cellular process response to stimulus signaling regulation of small GTPase mediated signal transduction Rac protein signal transduction biological regulation regulation of signal transduction intracellular signal transduction regulation of Rac protein signal transduction cell communication regulation of intracellular signal transduction cellular response to stimulus regulation of biological process regulation of signaling small GTPase-mediated signal transduction regulation of cellular process response to stimulus signaling regulation of small GTPase mediated signal transduction Rac protein signal transduction biological regulation regulation of signal transduction intracellular signal transduction regulation of Rac protein signal transduction cell communication regulation of intracellular signal transduction regulation of response to stimulus intracellular signaling cassette regulation of cell communication cellular process signal transduction 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 response to nutrient levels cellular response to nitrogen levels cellular response to starvation cellular response to nutrient levels cellular response to stress cellular response to nitrogen starvation response to stress response to starvation autophagosome assembly organelle assembly vacuole organization autophagosome organization cellular component biogenesis organelle organization cellular component assembly localization establishment of protein localization protein transport transport macromolecule localization intracellular protein localization establishment of localization positive regulation of protein K48-linked ubiquitination regulation of protein K48-linked ubiquitination regulation of protein modification process positive regulation of protein metabolic process positive regulation of biological process regulation of protein ubiquitination positive regulation of post-translational protein modification regulation of primary metabolic process positive regulation of metabolic process positive regulation of protein modification process protein ubiquitination positive regulation of macromolecule metabolic process protein metabolic process protein modification process regulation of protein modification by small protein conjugation or removal positive regulation of cellular process positive regulation of protein modification by small protein conjugation or removal positive regulation of protein ubiquitination regulation of protein polyubiquitination regulation of post-translational protein modification regulation of protein metabolic process protein polyubiquitination primary metabolic process regulation of macromolecule metabolic process positive regulation of protein polyubiquitination macromolecule modification macromolecule metabolic process post-translational protein modification protein modification by small protein conjugation regulation of metabolic process protein K48-linked ubiquitination protein modification by small protein conjugation or removal positive regulation of proteasomal protein catabolic process proteasome-mediated ubiquitin-dependent protein catabolic process regulation of ubiquitin-dependent protein catabolic process macromolecule catabolic process positive regulation of ubiquitin-dependent protein catabolic process modification-dependent macromolecule catabolic process proteasomal protein catabolic process protein catabolic process regulation of catabolic process positive regulation of protein catabolic process positive regulation of catabolic process regulation of proteasomal ubiquitin-dependent protein catabolic process modification-dependent protein catabolic process regulation of proteasomal protein catabolic process positive regulation of proteasomal ubiquitin-dependent protein catabolic process ubiquitin-dependent protein catabolic process regulation of protein catabolic process extrinsic apoptotic signaling pathway via death domain receptors cell surface receptor signaling pathway cell death extrinsic apoptotic signaling pathway apoptotic signaling pathway apoptotic process programmed cell death regulation of localization cellular localization protein localization to synapse regulation of protein localization regulation of neurotransmitter receptor localization to postsynaptic specialization membrane regulation of protein localization to synapse neurotransmitter receptor localization to postsynaptic specialization membrane regulation of biological quality regulation of protein localization to membrane regulation of receptor localization to synapse protein localization to postsynaptic specialization membrane protein localization to cell periphery protein localization to postsynaptic membrane regulation of protein localization to cell periphery localization within membrane protein localization to membrane protein-containing complex localization regulation of postsynaptic membrane neurotransmitter receptor levels regulation of cellular localization protein localization to organelle protein localization to postsynapse protein localization to cell junction receptor localization to synapse protein targeting trans-synaptic signaling synaptic signaling anterograde trans-synaptic signaling cell-cell signaling chemical synaptic transmission microtubule cytoskeleton organization microtubule-based process cytoskeleton organization mitophagy autophagy of mitochondrion	membrane-bounded organelle intracellular anatomical structure axoneme ciliary plasm cilium intracellular membraneless organelle plasma membrane bounded cell projection intracellular organelle cell projection cellular anatomical structure cytoskeleton organelle membraneless organelle cytoplasm membrane-bounded organelle intracellular anatomical structure axoneme ciliary plasm cilium intracellular membraneless organelle plasma membrane bounded cell projection intracellular organelle cell projection cellular anatomical structure cytoskeleton organelle membraneless organelle cytoplasm actin cytoskeleton cytosol cell periphery plasma membrane membrane endoplasmic reticulum smooth endoplasmic reticulum intracellular membrane-bounded organelle endomembrane system sperm midpiece 9+2 motile cilium sperm flagellum motile cilium lytic vacuole vacuole lysosome GABA-ergic synapse synapse cell junction cytoplasmic vesicle intracellular vesicle vesicle autophagosome vacuolar membrane autophagosome membrane bounding membrane of organelle organelle membrane Golgi membrane Golgi apparatus protein-containing complex microtubule associated complex microtubule cytoskeleton polymeric cytoskeletal fiber supramolecular fiber microtubule supramolecular polymer supramolecular complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
M, N, O, P, Q, M, N, O, P, Q, R, S, T, U, V, W [auth X]	IPR011256	Regulatory factor, effector binding domain superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	IPR004241	Autophagy protein Atg8 ubiquitin-like	Family
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	IPR029071	Ubiquitin-like domain superfamily	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
M, N, O, P, Q, M, N, O, P, Q, R, S, T, U, V, W [auth X]	: Q9Y6I9	IgA glomerulonephritis
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	: O95166	Hashimoto thyroiditis vascular disease hypothyroidism schizophrenia

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
M, N, O, P, Q, M, N, O, P, Q, R, S, T, U, V, W [auth X]	SEP	Parent Component: SER : AA0037 : O-phospho-L-serine MOD:00046

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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.