6KR4

Crystal structure of the liprin-alpha3_SAM123/LAR_D1D2 complex

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
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

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d6kr4a1	Alpha and beta proteins (a/b)	(Phosphotyrosine protein) phosphatases II	(Phosphotyrosine protein) phosphatases II	Higher-molecular-weight phosphotyrosine protein phosphatases	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d6kr4a3	Artifacts	Tags	Tags	Tags	N-terminal Tags	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d6kr4b1	Alpha and beta proteins (a/b)	(Phosphotyrosine protein) phosphatases II	(Phosphotyrosine protein) phosphatases II	Higher-molecular-weight phosphotyrosine protein phosphatases	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d6kr4b3	Artifacts	Tags	Tags	Tags	N-terminal Tags	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C	d6kr4c1	Alpha and beta proteins (a/b)	(Phosphotyrosine protein) phosphatases II	(Phosphotyrosine protein) phosphatases II	Higher-molecular-weight phosphotyrosine protein phosphatases	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C	d6kr4c3	Artifacts	Tags	Tags	Tags	N-terminal Tags	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D	d6kr4d1	Alpha and beta proteins (a/b)	(Phosphotyrosine protein) phosphatases II	(Phosphotyrosine protein) phosphatases II	Higher-molecular-weight phosphotyrosine protein phosphatases	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D	d6kr4d3	Artifacts	Tags	Tags	Tags	N-terminal Tags	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	(Phosphotyrosine protein) phosphatases II	8044351	3000304	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	(Phosphotyrosine protein) phosphatases II	8044353	3000304	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	(Phosphotyrosine protein) phosphatases II	8044353	3000304	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	(Phosphotyrosine protein) phosphatases II	8044351	3000304	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	(Phosphotyrosine protein) phosphatases II	8044351	3000304	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	(Phosphotyrosine protein) phosphatases II	8044353	3000304	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	(Phosphotyrosine protein) phosphatases II	8044351	3000304	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	(Phosphotyrosine protein) phosphatases II	8044353	3000304	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	PF00102	e6kr4A1	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Flavoproteins/Phosphotyrosine protein phosphatases-like	T: (Phosphotyrosine protein) phosphatases II	F: PF00102	ECOD (1.6)
B	PF00102	e6kr4B1	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Flavoproteins/Phosphotyrosine protein phosphatases-like	T: (Phosphotyrosine protein) phosphatases II	F: PF00102	ECOD (1.6)
C	PF00102	e6kr4C2	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Flavoproteins/Phosphotyrosine protein phosphatases-like	T: (Phosphotyrosine protein) phosphatases II	F: PF00102	ECOD (1.6)
D	PF00102	e6kr4D1	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Flavoproteins/Phosphotyrosine protein phosphatases-like	T: (Phosphotyrosine protein) phosphatases II	F: PF00102	ECOD (1.6)
E	PF00536	e6kr4E1	A: alpha arrays	X: HhH/H2TH	H: SAM/DNA-glycosylase	T: SAM domain-like	F: PF00536	ECOD (1.6)
E	PF07647	e6kr4E3	A: alpha arrays	X: HhH/H2TH	H: SAM/DNA-glycosylase	T: SAM domain-like	F: PF07647	ECOD (1.6)
F	PF00536	e6kr4F3	A: alpha arrays	X: HhH/H2TH	H: SAM/DNA-glycosylase	T: SAM domain-like	F: PF00536	ECOD (1.6)
F	PF07647	e6kr4F2	A: alpha arrays	X: HhH/H2TH	H: SAM/DNA-glycosylase	T: SAM domain-like	F: PF07647	ECOD (1.6)
G [auth H]	PF00536	e6kr4H3	A: alpha arrays	X: HhH/H2TH	H: SAM/DNA-glycosylase	T: SAM domain-like	F: PF00536	ECOD (1.6)
G [auth H]	PF07647	e6kr4H2	A: alpha arrays	X: HhH/H2TH	H: SAM/DNA-glycosylase	T: SAM domain-like	F: PF07647	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.90.190.10	Alpha Beta	Alpha-Beta Complex	Protein-Tyrosine Phosphatase	Chain A	CATH (utative)
B	3.90.190.10	Alpha Beta	Alpha-Beta Complex	Protein-Tyrosine Phosphatase	Chain A	CATH (utative)
C	3.90.190.10	Alpha Beta	Alpha-Beta Complex	Protein-Tyrosine Phosphatase	Chain A	CATH (utative)
D	3.90.190.10	Alpha Beta	Alpha-Beta Complex	Protein-Tyrosine Phosphatase	Chain A	CATH (utative)
E	1.10.150.50	Mainly Alpha	Orthogonal Bundle	DNA polymerase	domain 1	CATH (utative)
F	1.10.150.50	Mainly Alpha	Orthogonal Bundle	DNA polymerase	domain 1	CATH (utative)
G [auth H]	1.10.150.50	Mainly Alpha	Orthogonal Bundle	DNA polymerase	domain 1	CATH (utative)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF00102	Protein-tyrosine phosphatase (Y_phosphatase)	Protein-tyrosine phosphatase	-	Domain
E, F, G [auth H], H [auth G]	PF00536	SAM domain (Sterile alpha motif) (SAM_1)	SAM domain (Sterile alpha motif)	It has been suggested that SAM is an evolutionarily conserved protein binding domain that is involved in the regulation of numerous developmental processes in diverse eukaryotes. The SAM domain can potentially function as a protein interaction module ...	It has been suggested that SAM is an evolutionarily conserved protein binding domain that is involved in the regulation of numerous developmental processes in diverse eukaryotes. The SAM domain can potentially function as a protein interaction module through its ability to homo- and heterooligomerise with other SAM domains.	Domain
E, F, G [auth H], H [auth G]	PF07647	SAM domain (Sterile alpha motif) (SAM_2)	SAM domain (Sterile alpha motif)	-	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	Receptor-type tyrosine-protein phosphatase F	phosphoric ester hydrolase activity molecular transducer activity catalytic activity, acting on a protein phosphatase activity signaling receptor activity hydrolase activity phosphoprotein phosphatase activity hydrolase activity, acting on ester bonds protein tyrosine phosphatase activity transmembrane receptor protein phosphatase activity transmembrane signaling receptor activity transmembrane receptor protein tyrosine phosphatase activity catalytic activity cell adhesion molecule binding phosphoric ester hydrolase activity molecular transducer activity catalytic activity, acting on a protein phosphatase activity signaling receptor activity hydrolase activity phosphoprotein phosphatase activity hydrolase activity, acting on ester bonds protein tyrosine phosphatase activity transmembrane receptor protein phosphatase activity transmembrane signaling receptor activity transmembrane receptor protein tyrosine phosphatase activity catalytic activity cell adhesion molecule binding protein binding binding glycosaminoglycan binding proteoglycan binding chondroitin sulfate proteoglycan binding carbohydrate derivative binding sulfur compound binding protein-containing complex binding heparin binding	cellular component organization cell adhesion cell junction organization cell-cell adhesion cellular process synaptic membrane adhesion synapse organization cellular component organization or biogenesis cell-cell adhesion via plasma-membrane adhesion molecules cell migration cell motility negative regulation of receptor binding regulation of protein binding regulation of molecular function cellular component organization cell adhesion cell junction organization cell-cell adhesion cellular process synaptic membrane adhesion synapse organization cellular component organization or biogenesis cell-cell adhesion via plasma-membrane adhesion molecules cell migration cell motility negative regulation of receptor binding regulation of protein binding regulation of molecular function regulation of receptor binding negative regulation of protein binding regulation of binding negative regulation of binding biological regulation negative regulation of molecular function protein dephosphorylation organonitrogen compound metabolic process dephosphorylation cellular metabolic process primary metabolic process organic substance metabolic process macromolecule modification phosphate-containing compound metabolic process metabolic process protein metabolic process macromolecule metabolic process protein modification process phosphorus metabolic process peptidyl-tyrosine dephosphorylation cellular response to stimulus regulation of biological process regulation of cellular process cell surface receptor signaling pathway response to stimulus signaling cell communication cell surface receptor protein tyrosine phosphatase signaling pathway signal transduction enzyme-linked receptor protein signaling pathway regulation of neuron projection development multicellular organismal process regulation of cellular component organization regulation of developmental process cellular developmental process regulation of response to external stimulus cell projection organization regulation of cellular response to stress cell development neuron projection development regeneration response to axon injury neuron projection regeneration regulation of response to wounding neurogenesis multicellular organism development neuron differentiation cellular response to stress axon regeneration cell differentiation response to stress regulation of response to stress anatomical structure development response to wounding system development developmental process regulation of axon regeneration plasma membrane bounded cell projection organization regulation of cell projection organization response to external stimulus nervous system development axon development generation of neurons regulation of response to stimulus neuron development regulation of neuron projection regeneration regulation of plasma membrane bounded cell projection organization	extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region organelle extracellular space cellular anatomical entity vesicle extracellular membrane-bounded organelle cell periphery plasma membrane membrane cell projection extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region organelle extracellular space cellular anatomical entity vesicle extracellular membrane-bounded organelle cell periphery plasma membrane membrane cell projection neuron projection plasma membrane bounded cell projection somatodendritic compartment cell body neuronal cell body
E, F, G [auth H], H [auth G]	Liprin-alpha-3	-	cellular localization regulated exocytosis transport signaling synaptic vesicle cycle synaptic vesicle exocytosis membrane docking vesicle-mediated transport cell communication vesicle-mediated transport in synapse localization organelle localization by membrane tethering synaptic signaling secretion by cell organelle localization cellular localization regulated exocytosis transport signaling synaptic vesicle cycle synaptic vesicle exocytosis membrane docking vesicle-mediated transport cell communication vesicle-mediated transport in synapse localization organelle localization by membrane tethering synaptic signaling secretion by cell organelle localization signal release establishment of localization in cell vesicle docking involved in exocytosis trans-synaptic signaling regulation of biological process neurotransmitter secretion secretion biological regulation export from cell cell-cell signaling neurotransmitter transport synaptic vesicle docking establishment of localization chemical synaptic transmission signal release from synapse exocytosis anterograde trans-synaptic signaling vesicle docking exocytic process cellular process cellular component organization cell junction organization synapse organization cellular component organization or biogenesis regulation of neuronal synaptic plasticity regulation of synaptic plasticity regulation of short-term neuronal synaptic plasticity regulation of signaling regulation of cellular process modulation of chemical synaptic transmission regulation of trans-synaptic signaling regulation of cell communication regulation of biological quality	presynapse synapse cell junction cellular anatomical entity presynaptic active zone epididymosome membrane-bounded organelle extracellular vesicle extracellular organelle microvesicle extracellular region organelle vesicle extracellular membrane-bounded organelle presynapse synapse cell junction cellular anatomical entity presynaptic active zone epididymosome membrane-bounded organelle extracellular vesicle extracellular organelle microvesicle extracellular region organelle vesicle extracellular membrane-bounded organelle cell cortex intracellular anatomical structure cytoplasmic region presynaptic active zone cytoplasmic component cell periphery cell cortex region cytoplasm glutamatergic synapse acrosomal vesicle intracellular vesicle intracellular membrane-bounded organelle endomembrane system intracellular organelle cytoplasmic vesicle secretory granule secretory vesicle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR036179	Immunoglobulin-like domain superfamily	Homologous Superfamily
A, B, C, D	IPR003599	Immunoglobulin subtype	Domain
A, B, C, D	IPR003598	Immunoglobulin subtype 2	Domain
A, B, C, D	IPR003595	Protein-tyrosine phosphatase, catalytic	Domain
A, B, C, D	IPR013098	Immunoglobulin I-set	Domain
A, B, C, D	IPR016130	Protein-tyrosine phosphatase, active site	Active Site
A, B, C, D	IPR029021	Protein-tyrosine phosphatase-like	Homologous Superfamily
A, B, C, D	IPR003961	Fibronectin type III	Domain
A, B, C, D	IPR000242	Tyrosine-specific protein phosphatase, PTPase domain	Domain
A, B, C, D	IPR000387	Tyrosine-specific protein phosphatases domain	Domain
A, B, C, D	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
A, B, C, D	IPR007110	Immunoglobulin-like domain	Domain
A, B, C, D	IPR036116	Fibronectin type III superfamily	Homologous Superfamily
E, F, G [auth H], H [auth G]	IPR037621	Liprin-alpha, SAM domain repeat 2	Domain
E, F, G [auth H], H [auth G]	IPR013761	Sterile alpha motif/pointed domain superfamily	Homologous Superfamily
E, F, G [auth H], H [auth G]	IPR037620	Liprin-alpha, SAM domain repeat 1	Domain
E, F, G [auth H], H [auth G]	IPR037622	Liprin-alpha, SAM domain repeat 3	Domain
E, F, G [auth H], H [auth G]	IPR029515	LAR-interacting protein, Liprin	Family
E, F, G [auth H], H [auth G]	IPR001660	Sterile alpha motif domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B, C, D	Pharos: P10586	breasts and/or nipples, aplasia or hypoplasia of, 2 malignant mesothelioma Malignant neoplasm of stomach non-small cell lung carcinoma psoriasis adrenal cortex carcinoma autism spectrum disorder endogenous depression hereditary diffuse gastric adenocarcinoma lung cancer medulloblastoma ovarian cancer ulcerative colitis astrocytic tumor bipolar disorder breasts and/or nipples, aplasia or hypoplasia of, 2 malignant mesothelioma Malignant neoplasm of stomach non-small cell lung carcinoma psoriasis adrenal cortex carcinoma autism spectrum disorder endogenous depression hereditary diffuse gastric adenocarcinoma lung cancer medulloblastoma ovarian cancer ulcerative colitis astrocytic tumor bipolar disorder cutaneous lupus erythematosus gastric cancer interstitial cystitis myopathy pancreatic intraductal papillary-mucinous carcinoma attention deficit hyperactivity disorder, inattentive type cystic fibrosis Emery-Dreifuss muscular dystrophy gastric neoplasm lung adenocarcinoma

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 R01GM133198.