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Nicotinic receptor ligand binding domain-like superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   All beta proteins [ 48724] (174)
Fold:   Nicotinic receptor ligand binding domain-like [ 63711]
Superfamily:   Nicotinic receptor ligand binding domain-like [ 63712]
Families:   Nicotinic receptor ligand binding domain-like [ 63713]


Superfamily statistics
Genomes (209) Uniprot 2017_06 genome PDB chains (SCOP 1.75)
Domains 7,865 20,713 4
Proteins 7,674 20,179 4


Functional annotation
General category Regulation
Detailed category Signal transduction

Document:
Function annotation of SCOP domain superfamilies

Gene Ontology (high-quality)

(show details)
GO termFDR (singleton)FDR (all)SDFO levelAnnotation (direct or inherited)
Molecular Function (MF)transporter activity0.0000025270Moderately InformativeDirect
Molecular Function (MF)passive transmembrane transporter activity0.000000000091590InformativeDirect
Molecular Function (MF)molecular transducer activity0.000000042580InformativeDirect
Molecular Function (MF)signal transducer activity0.000000065630InformativeDirect
Molecular Function (MF)gated channel activity0.000000000000047920.000000000000001615Highly InformativeDirect
Molecular Function (MF)ion channel activity0.00000000000024190Highly InformativeDirect
Molecular Function (MF)transmembrane signaling receptor activity0.000000017490.00000001946Highly InformativeDirect

Document: GO annotation of SCOP domains

Gene Ontology (high-coverage)

(show details)
GO term FDR (all) SDFO level Annotation (direct or inherited)
Biological Process (BP) biological regulation 0.0000000007727 Least Informative Direct
Biological Process (BP) response to stimulus 0 Least Informative Direct
Biological Process (BP) multicellular organismal process 0.00001607 Least Informative Direct
Biological Process (BP) single-organism cellular process 0.05012 Least Informative Inherited
Biological Process (BP) cellular component organization or biogenesis 1 Least Informative Inherited
Biological Process (BP) cell communication 0 Moderately Informative Direct
Biological Process (BP) ion transport 0 Moderately Informative Direct
Biological Process (BP) single organism signaling 0 Moderately Informative Direct
Biological Process (BP) regulation of biological quality 0.00002368 Moderately Informative Direct
Biological Process (BP) cellular localization 1 Moderately Informative Inherited
Biological Process (BP) single-organism transport 1 Moderately Informative Inherited
Biological Process (BP) cellular response to chemical stimulus 1 Moderately Informative Inherited
Biological Process (BP) response to endogenous stimulus 0.5364 Moderately Informative Inherited
Biological Process (BP) response to oxygen-containing compound 1 Moderately Informative Inherited
Biological Process (BP) protein complex biogenesis 0.001038 Moderately Informative Inherited
Biological Process (BP) macromolecular complex subunit organization 0.06955 Moderately Informative Inherited
Biological Process (BP) cellular component assembly 0.3333 Moderately Informative Inherited
Biological Process (BP) regulation of signaling 1 Moderately Informative Inherited
Biological Process (BP) regulation of cell communication 1 Moderately Informative Inherited
Biological Process (BP) animal organ development 1 Moderately Informative Inherited
Biological Process (BP) immune system process 1 Moderately Informative Inherited
Biological Process (BP) response to abiotic stimulus 0.5893 Moderately Informative Inherited
Biological Process (BP) response to organic substance 0.00389 Moderately Informative Inherited
Biological Process (BP) regulation of localization 0.6005 Moderately Informative Inherited
Biological Process (BP) positive regulation of cellular process 1 Moderately Informative Inherited
Biological Process (BP) regulation of multicellular organismal process 0.435 Moderately Informative Inherited
Biological Process (BP) response to external stimulus 1 Moderately Informative Inherited
Biological Process (BP) response to nitrogen compound 0 Informative Direct
Biological Process (BP) behavior 0 Informative Direct
Biological Process (BP) system process 0 Informative Direct
Biological Process (BP) transmembrane transport 0 Informative Direct
Biological Process (BP) response to organic cyclic compound 0.000000000004858 Informative Direct
Biological Process (BP) regulation of system process 0.000001241 Informative Direct
Biological Process (BP) regulation of ion transport 0.00003717 Informative Direct
Biological Process (BP) cellular response to oxygen-containing compound 0.1577 Informative Inherited
Biological Process (BP) cellular chemical homeostasis 0.8929 Informative Inherited
Biological Process (BP) cation homeostasis 0.001396 Informative Inherited
Biological Process (BP) response to metal ion 0.0504 Informative Inherited
Biological Process (BP) cellular response to inorganic substance 0.01509 Informative Inherited
Biological Process (BP) inorganic ion homeostasis 0.001612 Informative Inherited
Biological Process (BP) protein oligomerization 0.001492 Informative Inherited
Biological Process (BP) response to acid chemical 0.2154 Informative Inherited
Biological Process (BP) regulation of locomotion 0.4446 Informative Inherited
Biological Process (BP) response to temperature stimulus 0.2722 Informative Inherited
Biological Process (BP) cell activation 0.3778 Informative Inherited
Biological Process (BP) positive regulation of transport 0.04188 Informative Inherited
Biological Process (BP) negative regulation of multicellular organismal process 0.2872 Informative Inherited
Biological Process (BP) regulation of cytokine production 0.6279 Informative Inherited
Biological Process (BP) locomotion 0.009716 Informative Inherited
Biological Process (BP) regulation of secretion 0.05522 Informative Inherited
Biological Process (BP) response to radiation 0.9941 Informative Inherited
Biological Process (BP) anion transport 0.1223 Informative Inherited
Biological Process (BP) metal ion transport 1 Informative Inherited
Biological Process (BP) regulation of membrane potential 0 Highly Informative Direct
Biological Process (BP) cell-cell signaling 0 Highly Informative Direct
Biological Process (BP) single-organism behavior 0 Highly Informative Direct
Biological Process (BP) anion transmembrane transport 0.0000000000001817 Highly Informative Direct
Biological Process (BP) G-protein coupled receptor signaling pathway 0.00000000001016 Highly Informative Direct
Biological Process (BP) cellular calcium ion homeostasis 0.000002343 Highly Informative Direct
Biological Process (BP) response to hypoxia 0.000007076 Highly Informative Direct
Biological Process (BP) response to amino acid 0.0000101 Highly Informative Direct
Biological Process (BP) anatomical structure homeostasis 0.0004272 Highly Informative Direct
Biological Process (BP) cellular response to organonitrogen compound 0.000452 Highly Informative Direct
Biological Process (BP) muscle system process 0.0005161 Highly Informative Direct
Biological Process (BP) inorganic cation transmembrane transport 1 Highly Informative Inherited
Biological Process (BP) import into cell 0.03636 Highly Informative Inherited
Biological Process (BP) regulation of reproductive process 0.0365 Highly Informative Inherited
Biological Process (BP) response to alcohol 0.09058 Highly Informative Inherited
Biological Process (BP) lymphocyte activation 0.0734 Highly Informative Inherited
Biological Process (BP) positive regulation of secretion by cell 0.009624 Highly Informative Inherited
Biological Process (BP) positive regulation of ion transport 0.002069 Highly Informative Inherited
Biological Process (BP) negative regulation of cytokine production 0.007994 Highly Informative Inherited
Biological Process (BP) locomotory behavior 0.01251 Highly Informative Inherited
Biological Process (BP) nervous system process 0.04426 Highly Informative Inherited
Biological Process (BP) divalent inorganic cation transport 0.9473 Highly Informative Inherited
Molecular Function (MF) binding 1 Least Informative Inherited
Molecular Function (MF) transporter activity 0 Moderately Informative Direct
Molecular Function (MF) small molecule binding 0.1444 Moderately Informative Inherited
Molecular Function (MF) anion binding 1 Moderately Informative Inherited
Molecular Function (MF) passive transmembrane transporter activity 0 Informative Direct
Molecular Function (MF) molecular transducer activity 0 Informative Direct
Molecular Function (MF) signal transducer activity 0 Informative Direct
Molecular Function (MF) carboxylic acid binding 0.00000000191 Informative Direct
Molecular Function (MF) anion transmembrane transporter activity 0.00002296 Informative Direct
Molecular Function (MF) gated channel activity 0.000000000000001615 Highly Informative Direct
Molecular Function (MF) ion channel activity 0 Highly Informative Direct
Molecular Function (MF) transmembrane signaling receptor activity 0.00000001946 Highly Informative Direct
Molecular Function (MF) ammonium ion binding 0 Highly Informative Direct
Molecular Function (MF) inorganic anion transmembrane transporter activity 0 Highly Informative Direct
Molecular Function (MF) amino acid binding 0.000000000000004728 Highly Informative Direct
Molecular Function (MF) drug binding 0.00000000000000853 Highly Informative Direct
Cellular Component (CC) membrane 0 Least Informative Direct
Cellular Component (CC) cell projection 0 Moderately Informative Direct
Cellular Component (CC) intrinsic component of membrane 0 Moderately Informative Direct
Cellular Component (CC) plasma membrane 0 Moderately Informative Direct
Cellular Component (CC) transporter complex 0 Informative Direct
Cellular Component (CC) neuron projection 0 Informative Direct
Cellular Component (CC) plasma membrane region 0.03677 Informative Inherited
Cellular Component (CC) intrinsic component of plasma membrane 0 Highly Informative Direct
Cellular Component (CC) neuronal cell body 0 Highly Informative Direct
Cellular Component (CC) receptor complex 0 Highly Informative Direct
Cellular Component (CC) dendrite 0.0000000000000228 Highly Informative Direct

Document: GO annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processTransport0Least InformativeDirect
Biological processIon transport0Moderately InformativeDirect
Cellular componentMembrane0Least InformativeDirect
Cellular componentCell junction0Moderately InformativeDirect
Cellular componentCell membrane0Moderately InformativeDirect
Cellular componentCytoplasmic vesicle0Moderately InformativeDirect
Cellular componentCell projection0.0000000000001503Moderately InformativeDirect
Cellular componentSynapse0InformativeDirect
Cellular componentPostsynaptic cell membrane0Highly InformativeDirect
DiseaseDisease mutation0.000000000004455Least InformativeDirect
DiseaseEpilepsy0.000000006947InformativeDirect
DomainSignal0Least InformativeDirect
DomainTransmembrane0Least InformativeDirect
Molecular functionChloride0InformativeDirect
Molecular functionChloride channel0Highly InformativeDirect
Post-translational modificationReceptor0Moderately InformativeDirect
Post-translational modificationIon channel0InformativeDirect
Post-translational modificationLigand-gated ion channel0Highly InformativeDirect
Post-translational modificationGlycoprotein0Least InformativeDirect
Post-translational modificationDisulfide bond0Least InformativeDirect
Post-translational modificationPalmitate0.0000000001538Moderately InformativeDirect

Document: KW annotation of SCOP domains

InterPro annotation
Cross references IPR006202 SSF63712 Protein matches
Abstract

This entry presents the extracellular ligand binding domain of these ion channels. This domain forms a pentameric arrangement in the known structure.


InterPro database


PDBeMotif information about ligands, sequence and structure motifs
Cross references PDB entries
Ligand binding statistics
Nucleic-acid binding statistics
Occurrence of secondary structure elements
Occurrence of small 3D structural motifs

PDBeMotif resource

Jump to [ Top of page · SCOP classification · InterPro annotation · PDBeMotif links · Functional annotation · Gene Ontology (high-quality) · Gene Ontology (high-coverage) · UniProtKB KeyWords (KW) ]

Internal database links

Browse genome assignments for this superfamily. The SUPERFAMILY hidden Markov model library has been used to carry out SCOP domain assignments to all genomes at the superfamily level.


Alignments of sequences to 1 models in this superfamily are available by clicking on the 'Alignments' icon above. PDB sequences less than 40% identical are shown by default, but any other sequence(s) may be aligned. Select PDB sequences, genome sequences, or paste in or upload your own sequences.


Browse and view proteins in genomes which have different domain combinations including a Nicotinic receptor ligand binding domain-like domain.


Examine the distribution of domain superfamilies, or families, across the major taxonomic kingdoms or genomes within a kingdom. This gives an immediate impression of how superfamilies, or families, are restricted to certain kingdoms of life.


Explore domain occurrence network where nodes represent genomes and edges are domain architectures (shared between genomes) containing the superfamily of interest.

There are 1 hidden Markov models representing the Nicotinic receptor ligand binding domain-like superfamily. Information on how the models are built, and plots showing hydrophobicity, match emmission probabilities and insertion/deletion probabilities can be inspected.


Jump to [ Top of page · SCOP classification · InterPro annotation · PDBeMotif links · Functional annotation · Gene Ontology (high-quality) · Gene Ontology (high-coverage) · UniProtKB KeyWords (KW) · Internal database links ]