5V5V | pdb_00005v5v

Complex of NLGN2 with MDGA1 Ig1-Ig2

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

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
G [auth F]	SCOP2B Superfamily	alpha/beta-Hydrolases	8071850	3000102	SCOP2B (2022-06-29)
F [auth E]	SCOP2B Superfamily	alpha/beta-Hydrolases	8071850	3000102	SCOP2B (2022-06-29)
E [auth D]	SCOP2B Superfamily	alpha/beta-Hydrolases	8071850	3000102	SCOP2B (2022-06-29)
D [auth C]	SCOP2B Superfamily	alpha/beta-Hydrolases	8071850	3000102	SCOP2B (2022-06-29)
C [auth B]	SCOP2B Superfamily	alpha/beta-Hydrolases	8071850	3000102	SCOP2B (2022-06-29)
A	SCOP2 Family	Acetylcholinesterase-like	8071849	4000699	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	alpha/beta-Hydrolases	8071850	3000102	SCOP2 (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	I-set_5	e5v5vL2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: I-set_5	ECOD (1.6)
L	I-set_2	e5v5vL1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: I-set_2	ECOD (1.6)
K	I-set_5	e5v5vK2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: I-set_5	ECOD (1.6)
K	I-set_2	e5v5vK1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: I-set_2	ECOD (1.6)
J	I-set_5	e5v5vJ2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: I-set_5	ECOD (1.6)
J	I-set_2	e5v5vJ1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: I-set_2	ECOD (1.6)
I	I-set_5	e5v5vI1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: I-set_5	ECOD (1.6)
I	I-set_2	e5v5vI2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: I-set_2	ECOD (1.6)
H	I-set_5	e5v5vH1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: I-set_5	ECOD (1.6)
H	I-set_2	e5v5vH2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: I-set_2	ECOD (1.6)
B [auth G]	I-set_5	e5v5vG2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: I-set_5	ECOD (1.6)
B [auth G]	I-set_2	e5v5vG1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: I-set_2	ECOD (1.6)
G [auth F]	COesterase	e5v5vF1	A: a/b three-layered sandwiches	X: alpha/beta-Hydrolases (From Topology)	H: alpha/beta-Hydrolases (From Topology)	T: alpha/beta-Hydrolases	F: COesterase	ECOD (1.6)
F [auth E]	COesterase	e5v5vE1	A: a/b three-layered sandwiches	X: alpha/beta-Hydrolases (From Topology)	H: alpha/beta-Hydrolases (From Topology)	T: alpha/beta-Hydrolases	F: COesterase	ECOD (1.6)
E [auth D]	COesterase	e5v5vD1	A: a/b three-layered sandwiches	X: alpha/beta-Hydrolases (From Topology)	H: alpha/beta-Hydrolases (From Topology)	T: alpha/beta-Hydrolases	F: COesterase	ECOD (1.6)
D [auth C]	COesterase	e5v5vC1	A: a/b three-layered sandwiches	X: alpha/beta-Hydrolases (From Topology)	H: alpha/beta-Hydrolases (From Topology)	T: alpha/beta-Hydrolases	F: COesterase	ECOD (1.6)
C [auth B]	COesterase	e5v5vB1	A: a/b three-layered sandwiches	X: alpha/beta-Hydrolases (From Topology)	H: alpha/beta-Hydrolases (From Topology)	T: alpha/beta-Hydrolases	F: COesterase	ECOD (1.6)
A	COesterase	e5v5vA1	A: a/b three-layered sandwiches	X: alpha/beta-Hydrolases (From Topology)	H: alpha/beta-Hydrolases (From Topology)	T: alpha/beta-Hydrolases	F: COesterase	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B [auth G], H, I, J, K, B [auth G], H, I, J, K, L	PF13927	Immunoglobulin domain (Ig_3)	Immunoglobulin domain	This family contains immunoglobulin-like domains.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B [auth G], H, I, J, K, B [auth G], H, I, J, K, L	MAM domain-containing glycosylphosphatidylinositol anchor protein 1	-	developmental process multicellular organism development multicellular organismal process head development central nervous system development anatomical structure development animal organ development brain development nervous system development system development regulation of cellular component organization regulation of cellular process regulation of presynapse assembly cellular component organization developmental process multicellular organism development multicellular organismal process head development central nervous system development anatomical structure development animal organ development brain development nervous system development system development regulation of cellular component organization regulation of cellular process regulation of presynapse assembly cellular component organization cellular component biogenesis cellular component assembly regulation of presynapse organization cell junction assembly regulation of synapse structure or activity regulation of synapse assembly synapse organization cellular component organization or biogenesis regulation of biological quality regulation of biological process biological regulation presynapse organization regulation of cellular component biogenesis regulation of cell junction assembly regulation of synapse organization cell junction organization cellular process synapse assembly presynapse assembly cerebral cortex cell migration forebrain development cerebral cortex radially oriented cell migration pallium development cerebral cortex development telencephalon cell migration forebrain cell migration cell migration telencephalon development cell motility spinal cord association neuron differentiation cellular developmental process dorsal spinal cord development cell differentiation in spinal cord generation of neurons central nervous system neuron differentiation neurogenesis spinal cord development neuron differentiation cell differentiation inhibitory synapse assembly regulation of cell adhesion regulation of synaptic membrane adhesion cell adhesion cell-cell adhesion regulation of cell-cell adhesion synaptic membrane adhesion neuron migration	cell surface cellular anatomical structure cell periphery plasma membrane membrane somatodendritic compartment cell projection dendrite dendritic tree neuron projection plasma membrane bounded cell projection GABA-ergic synapse synapse cell junction cell surface cellular anatomical structure cell periphery plasma membrane membrane somatodendritic compartment cell projection dendrite dendritic tree neuron projection plasma membrane bounded cell projection GABA-ergic synapse synapse cell junction side of membrane membrane-bounded organelle intracellular organelle intracellular anatomical structure Golgi apparatus organelle cytoplasm intracellular membrane-bounded organelle endomembrane system extracellular region axon extracellular space
A, C [auth B], D [auth C], E [auth D], F [auth E], A, C [auth B], D [auth C], E [auth D], F [auth E], G [auth F]	Neuroligin-2	protein binding binding signaling receptor binding neurexin family protein binding identical protein binding cell adhesion molecule binding	cellular response to stimulus positive regulation of cell communication multicellular organismal process regulation of postsynaptic membrane potential system process regulation of cellular process positive regulation of signal transduction response to stimulus signaling modulation of chemical synaptic transmission regulation of system process positive regulation of excitatory postsynaptic potential positive regulation of biological process regulation of signal transduction chemical synaptic transmission, postsynaptic cellular response to stimulus positive regulation of cell communication multicellular organismal process regulation of postsynaptic membrane potential system process regulation of cellular process positive regulation of signal transduction response to stimulus signaling modulation of chemical synaptic transmission regulation of system process positive regulation of excitatory postsynaptic potential positive regulation of biological process regulation of signal transduction chemical synaptic transmission, postsynaptic cell communication positive regulation of response to stimulus synaptic signaling modulation of excitatory postsynaptic potential regulation of multicellular organismal process signal transduction regulation of biological quality positive regulation of cellular process trans-synaptic signaling regulation of biological process regulation of signaling cell surface receptor signaling pathway nervous system process biological regulation cell-cell signaling chemical synaptic transmission regulation of nervous system process regulation of trans-synaptic signaling regulation of response to stimulus anterograde trans-synaptic signaling regulation of cell communication cellular process excitatory postsynaptic potential regulation of membrane potential positive regulation of signaling behavior thigmotaxis positive regulation of inhibitory postsynaptic potential positive regulation of nervous system process modulation of inhibitory postsynaptic potential inhibitory postsynaptic potential positive regulation of multicellular organismal process membrane organization cellular localization postsynapse organization localization within membrane protein localization to membrane cellular component organization localization organelle organization postsynaptic density protein 95 clustering cell junction organization postsynaptic density organization macromolecule localization cellular component organization or biogenesis synapse organization postsynaptic specialization organization intracellular protein localization postsynaptic membrane organization regulation of developmental process cellular developmental process cell projection organization positive regulation of dendritic spine development cell development regulation of dendritic spine development neuron projection development positive regulation of developmental process neurogenesis multicellular organism development neuron differentiation dendrite development cell differentiation anatomical structure development system development developmental process dendritic spine development plasma membrane bounded cell projection organization nervous system development generation of neurons neuron development cell adhesion cell-cell adhesion neuron cell-cell adhesion inhibitory synapse assembly cellular component biogenesis cellular component assembly cell junction assembly synapse assembly neurotransmitter-gated ion channel clustering receptor clustering presynapse organization presynapse assembly terminal button organization regulation of localization protein localization to synapse regulation of protein localization positive regulation of protein localization to synapse regulation of protein localization to synapse positive regulation of protein localization protein localization to cell junction positive regulation of nervous system development positive regulation of cellular component organization regulation of cellular component organization regulation of nervous system development regulation of synapse structure or activity regulation of synapse assembly regulation of multicellular organismal development positive regulation of cellular component biogenesis regulation of cellular component biogenesis regulation of cell junction assembly positive regulation of cell junction assembly regulation of synapse organization positive regulation of synapse assembly organelle assembly postsynaptic specialization assembly postsynapse assembly metabolic process primary metabolic process protein metabolic process macromolecule metabolic process insulin metabolic process synaptic transmission, glutamatergic regulation of synaptic transmission, glutamatergic positive regulation of synaptic transmission positive regulation of synaptic transmission, glutamatergic membrane biogenesis presynaptic membrane assembly membrane assembly presynaptic membrane organization protein localization to cell surface positive regulation of synaptic transmission, GABAergic synaptic transmission, GABAergic regulation of synaptic transmission, GABAergic regulation of presynapse assembly regulation of presynapse organization respiratory gaseous exchange by respiratory system respiratory system process regulation of respiratory gaseous exchange regulation of respiratory system process regulation of respiratory gaseous exchange by nervous system process vesicle localization transport regulation of transport synaptic vesicle clustering synaptic vesicle cycle establishment of localization vesicle-mediated transport vesicle-mediated transport in synapse positive regulation of transport organelle localization establishment of localization in cell positive regulation of synaptic vesicle clustering regulation of synaptic vesicle clustering synaptic vesicle localization neuromuscular process neuromuscular process controlling balance positive regulation of protein localization to membrane t-SNARE clustering positive regulation of t-SNARE clustering regulation of cellular localization regulation of t-SNARE clustering regulation of protein localization to membrane adult locomotory behavior adult behavior locomotory behavior jump response exploration behavior locomotory exploration behavior cell population proliferation positive regulation of cell population proliferation regulation of cell population proliferation biological process involved in intraspecies interaction between organisms social behavior postsynaptic membrane assembly sensory perception sensory perception of pain establishment of protein localization nitrogen compound transport positive regulation of establishment of protein localization positive regulation of insulin secretion regulation of peptide hormone secretion regulation of hormone levels positive regulation of peptide hormone secretion establishment of protein localization to extracellular region protein secretion regulation of protein secretion regulation of secretion regulation of hormone secretion regulation of peptide secretion positive regulation of secretion by cell hormone secretion protein localization to extracellular region positive regulation of protein transport peptide secretion regulation of secretion by cell secretion by cell positive regulation of hormone secretion positive regulation of secretion amide transport signal release positive regulation of peptide secretion secretion regulation of peptide transport regulation of establishment of protein localization export from cell regulation of protein transport positive regulation of protein secretion peptide transport protein transport regulation of insulin secretion peptide hormone secretion hormone transport insulin secretion excitatory synapse assembly gephyrin clustering involved in postsynaptic density assembly postsynaptic density assembly	cell periphery postsynapse cellular anatomical structure postsynaptic membrane synapse cell junction membrane plasma membrane plasma membrane region synaptic membrane presynapse presynaptic membrane somatodendritic compartment cell projection cell periphery postsynapse cellular anatomical structure postsynaptic membrane synapse cell junction membrane plasma membrane plasma membrane region synaptic membrane presynapse presynaptic membrane somatodendritic compartment cell projection dendrite dendritic tree neuron projection plasma membrane bounded cell projection dopaminergic synapse dendritic shaft axon inhibitory synapse cell surface glycinergic synapse postsynaptic specialization membrane postsynaptic specialization organelle GABA-ergic synapse ribbon synapse excitatory synapse

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B [auth G], H, I, J, K, B [auth G], H, I, J, K, L	IPR036179	Immunoglobulin-like domain superfamily	Homologous Superfamily
B [auth G], H, I, J, K, B [auth G], H, I, J, K, L	IPR003598	Immunoglobulin subtype 2	Domain
B [auth G], H, I, J, K, B [auth G], H, I, J, K, L	IPR013320	Concanavalin A-like lectin/glucanase domain superfamily	Homologous Superfamily
B [auth G], H, I, J, K, B [auth G], H, I, J, K, L	IPR000998	MAM domain	Domain
B [auth G], H, I, J, K, B [auth G], H, I, J, K, L	IPR003599	Immunoglobulin domain subtype	Domain
B [auth G], H, I, J, K, B [auth G], H, I, J, K, L	IPR013098	Immunoglobulin I-set	Domain
B [auth G], H, I, J, K, B [auth G], H, I, J, K, L	IPR050958	Cell Adhesion and Cytoskeletal Organization	Family
B [auth G], H, I, J, K, B [auth G], H, I, J, K, L	IPR003961	Fibronectin type III	Domain
B [auth G], H, I, J, K, B [auth G], H, I, J, K, L	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
B [auth G], H, I, J, K, B [auth G], H, I, J, K, L	IPR007110	Immunoglobulin-like domain	Domain
B [auth G], H, I, J, K, B [auth G], H, I, J, K, L	IPR036116	Fibronectin type III superfamily	Homologous Superfamily
A, C [auth B], D [auth C], E [auth D], F [auth E], A, C [auth B], D [auth C], E [auth D], F [auth E], G [auth F]	IPR051093	Neuroligin and Bile salt-activated lipase	Family
A, C [auth B], D [auth C], E [auth D], F [auth E], A, C [auth B], D [auth C], E [auth D], F [auth E], G [auth F]	IPR002018	Carboxylesterase, type B	Domain
A, C [auth B], D [auth C], E [auth D], F [auth E], A, C [auth B], D [auth C], E [auth D], F [auth E], G [auth F]	IPR019819	Carboxylesterase type B, conserved site	Conserved Site
A, C [auth B], D [auth C], E [auth D], F [auth E], A, C [auth B], D [auth C], E [auth D], F [auth E], G [auth F]	IPR000460	Neuroligin	Family
A, C [auth B], D [auth C], E [auth D], F [auth E], A, C [auth B], D [auth C], E [auth D], F [auth E], G [auth F]	IPR029058	Alpha/Beta hydrolase fold	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
B [auth G], H, I, J, K, B [auth G], H, I, J, K, L	Pharos: Q8NFP4	bipolar disorder schizophrenia major depressive disorder Unipolar Depression ovarian cancer

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.