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SH3-domain superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   All beta proteins [ 48724] (174)
Fold:   SH3-like barrel [ 50036] (21)
Superfamily:   SH3-domain [ 50044]
Families:   SH3-domain [ 50045] (39)


Superfamily statistics
Genomes (733) Uniprot 2018_03 genome PDB chains (SCOP 1.75)
Domains 39,669 125,642 127
Proteins 30,833 97,806 122


Functional annotation
General category Regulation
Detailed category Signal transduction

Document:
Function annotation of SCOP domain superfamilies

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEO levelAnnotation (direct or inherited)
Enzyme Commission (EC)Acting on ester bonds0.4052Least InformativeInherited
Enzyme Commission (EC)Phosphoric diester hydrolases0.00000006272Moderately InformativeDirect
Enzyme Commission (EC)Protein-serine/threonine kinases0.0001767Moderately InformativeDirect
Enzyme Commission (EC)Glycosyltransferases1Moderately InformativeInherited
Enzyme Commission (EC)Non-specific protein-tyrosine kinase0InformativeDirect
Enzyme Commission (EC)Phosphoinositide phospholipase C0.000000000000003251InformativeDirect
Enzyme Commission (EC)Mitogen-activated protein kinase kinase kinase0.0000000000002472Highly InformativeDirect

Document: EC annotation of SCOP domains

Human Phenotype (HP)

(show details)
HP termFDR (all)SDHP levelAnnotation (direct or inherited)
Phenotypic Abnormality (PA)Abnormality of the digestive system0.6149Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of connective tissue0.2223Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the abdominal organs0.4165Moderately InformativeInherited
Phenotypic Abnormality (PA)Cellulitis0.000202Highly InformativeDirect

Document: HP annotation of SCOP domains

Mouse Phenotype (MP)

(show details)
MP termFDR (all)SDMP levelAnnotation (direct or inherited)
Mammalian Phenotype (MP)hematopoietic system phenotype0.01006Least InformativeInherited
Mammalian Phenotype (MP)immune system phenotype0.0408Least InformativeInherited
Mammalian Phenotype (MP)nervous system phenotype0.05975Least InformativeInherited
Mammalian Phenotype (MP)cardiovascular system phenotype0.7619Least InformativeInherited
Mammalian Phenotype (MP)abnormal immune serum protein physiology0.07271Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal nervous system physiology0.08776Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal leukocyte physiology0.1455Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal mononuclear cell morphology0.1668Moderately InformativeInherited
Mammalian Phenotype (MP)hearing/vestibular/ear phenotype0.1956Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal blood cell morphology/development0.2779Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal blood vessel morphology0.4817Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal brain morphology0.5878Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal blood cell morphology0.7993Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal somatic nervous system morphology0.8126Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal professional antigen presenting cell physiology0.8152Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal metabolism0.963Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal B cell proliferation0.0002686InformativeDirect
Mammalian Phenotype (MP)abnormal cerebral hemisphere morphology0.08869InformativeInherited
Mammalian Phenotype (MP)abnormal limbic system morphology0.1105InformativeInherited
Mammalian Phenotype (MP)abnormal enzyme/coenzyme activity0.2853InformativeInherited
Mammalian Phenotype (MP)abnormal neuron physiology0.2893InformativeInherited
Mammalian Phenotype (MP)abnormal CNS synaptic transmission0.3472InformativeInherited
Mammalian Phenotype (MP)abnormal cochlear hair cell morphology0.3785InformativeInherited
Mammalian Phenotype (MP)abnormal interleukin secretion0.3887InformativeInherited
Mammalian Phenotype (MP)abnormal T cell differentiation0.4027InformativeInherited
Mammalian Phenotype (MP)abnormal effector T cell morphology0.4623InformativeInherited
Mammalian Phenotype (MP)abnormal alpha-beta T cell morphology0.5159InformativeInherited
Mammalian Phenotype (MP)abnormal synaptic vesicle recycling0.000008223Highly InformativeDirect
Mammalian Phenotype (MP)abnormal interleukin-2 secretion0.0004406Highly InformativeDirect
Mammalian Phenotype (MP)decreased excitatory postsynaptic current amplitude0.0005052Highly InformativeDirect
Mammalian Phenotype (MP)abnormal hippocampus pyramidal cell layer0.0009515Highly InformativeDirect
Mammalian Phenotype (MP)abnormal granulocyte physiology0.05874Highly InformativeInherited
Mammalian Phenotype (MP)abnormal cochlear hair cell stereociliary bundle morphology0.08478Highly InformativeInherited
Mammalian Phenotype (MP)abnormal CD8-positive, alpha beta T cell morphology0.2802Highly InformativeInherited

Document: MP annotation of SCOP domains

Worm Phenotype (WP)

(show details)
WP termFDR (all)SDWP levelAnnotation (direct or inherited)
Worm Phenotype (WP)cell morphology variant0.000001852Least InformativeDirect
Worm Phenotype (WP)organ system morphology variant0.00001082Least InformativeDirect
Worm Phenotype (WP)blast cell physiology variant0.00003073Least InformativeDirect
Worm Phenotype (WP)cell physiology variant0.00003099Least InformativeDirect
Worm Phenotype (WP)organism environmental stimulus response variant0.01323Least InformativeInherited
Worm Phenotype (WP)organism behavior variant0.01484Least InformativeInherited
Worm Phenotype (WP)organism metabolism processing variant0.04061Least InformativeInherited
Worm Phenotype (WP)protein expression variant0.00000001391Moderately InformativeDirect
Worm Phenotype (WP)apoptosis variant0.00003894Moderately InformativeDirect
Worm Phenotype (WP)drug response variant0.06098Moderately InformativeInherited
Worm Phenotype (WP)cell organization biogenesis variant0.5645Moderately InformativeInherited
Worm Phenotype (WP)germ cell morphology variant0.7813Moderately InformativeInherited
Worm Phenotype (WP)body wall muscle sarcomere morphology variant0.000000000006446InformativeDirect
Worm Phenotype (WP)muscle cell physiology variant0.00000000006886InformativeDirect
Worm Phenotype (WP)mitochondria morphology variant0.000000188InformativeDirect
Worm Phenotype (WP)cell component localization variant0.00002629InformativeDirect
Worm Phenotype (WP)aldicarb response variant0.00008176InformativeDirect
Worm Phenotype (WP)level of protein expression variant0.00893InformativeInherited
Worm Phenotype (WP)oocyte morphology variant1InformativeInherited
Worm Phenotype (WP)protein expression reduced0.00000000001119Highly InformativeDirect
Worm Phenotype (WP)body elongation variant0.0002491Highly InformativeDirect
Worm Phenotype (WP)endomitotic oocytes0.000489Highly InformativeDirect
Worm Phenotype (WP)ovulation variant0.0006107Highly InformativeDirect
Worm Phenotype (WP)cytoskeleton organization biogenesis variant0.03774Highly InformativeInherited

Document: WP annotation of SCOP domains

Yeast Phenotype (YP)

(show details)
YP termFDR (all)SDYP levelAnnotation (direct or inherited)
Yeast Phenotype (YP)morphology0.1488Moderately InformativeInherited
Yeast Phenotype (YP)intracellular transport0.00002112InformativeDirect
Yeast Phenotype (YP)subcellular morphology0.3133InformativeInherited
Yeast Phenotype (YP)chitin deposition0.0003534Highly InformativeDirect

Document: YP annotation of SCOP domains

Fly Phenotype (FP)

(show details) Document: FP annotation of SCOP domains

Fly Anatomy (FA)

(show details) Document: FA annotation of SCOP domains

Zebrafish Anatomy (ZA)

(show details) Document: ZA annotation of SCOP domains

Xenopus Anatomy (XA)

(show details) Document: XA annotation of SCOP domains

Arabidopsis Plant Ontology (AP)

(show details)
AP termFDR (all)SDAP levelAnnotation (direct or inherited)
Plant ANatomical entity (PAN)whole plant0Least InformativeDirect
Plant ANatomical entity (PAN)guard cell0Least InformativeDirect
Plant ANatomical entity (PAN)seed0Least InformativeDirect
Plant ANatomical entity (PAN)portion of meristem tissue0Least InformativeDirect
Plant ANatomical entity (PAN)megasporophyll0Least InformativeDirect
Plant ANatomical entity (PAN)microsporophyll0Least InformativeDirect
Plant ANatomical entity (PAN)flower0Least InformativeDirect
Plant ANatomical entity (PAN)inflorescence0Least InformativeDirect
Plant ANatomical entity (PAN)collective phyllome structure0Least InformativeDirect
Plant ANatomical entity (PAN)root system0Least InformativeDirect
Plant ANatomical entity (PAN)shoot axis0Least InformativeDirect
Plant ANatomical entity (PAN)leaf0Least InformativeDirect
Plant ANatomical entity (PAN)sporangium0Least InformativeDirect
Plant ANatomical entity (PAN)cardinal part of multi-tissue plant structure0Least InformativeDirect
Plant ANatomical entity (PAN)inflorescence meristem0Moderately InformativeDirect
Plant ANatomical entity (PAN)cotyledon0Moderately InformativeDirect
Plant ANatomical entity (PAN)pollen0Moderately InformativeDirect
Plant structure DEvelopment stage (PDE)4 leaf senescence stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)E expanded cotyledon stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)F mature embryo stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)C globular stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)D bilateral stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.12 twelve leaves visible stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.08 eight leaves visible stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.02 two leaves visible stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.10 ten leaves visible stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.04 four leaves visible stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.06 six leaves visible stage0Least InformativeDirect

Document: AP annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEC levelAnnotation (direct or inherited)
Enzyme Commission (EC)Transferring phosphorus-containing groups0Least InformativeDirect
Enzyme Commission (EC)Hydrolases1Least InformativeInherited
Enzyme Commission (EC)Aminoacyltransferases0.00000003542Moderately InformativeDirect
Enzyme Commission (EC)Protein-serine/threonine kinases0.00003138Moderately InformativeDirect
Enzyme Commission (EC)Transferring one-carbon groups1Moderately InformativeInherited
Enzyme Commission (EC)Glycosyltransferases1Moderately InformativeInherited
Enzyme Commission (EC)Protein-tyrosine kinases0InformativeDirect
Enzyme Commission (EC)RING-type E3 ubiquitin transferase0.00000000002226InformativeDirect
Enzyme Commission (EC)Phosphoric diester hydrolases0.00000002089InformativeDirect
Enzyme Commission (EC)Hexosyltransferases0.0001128InformativeDirect
Enzyme Commission (EC)Non-specific protein-tyrosine kinase0Highly InformativeDirect
Enzyme Commission (EC)Phosphoinositide phospholipase C0Highly InformativeDirect

Document: EC annotation of SCOP domains

InterPro annotation
Cross references IPR001452 SSF50044 Protein matches
Abstract SH3 (src Homology-3) domains are small protein modules containing approximately 50 amino acid residues [PubMed15335710, PubMed11256992]. They are found in a great variety of intracellular or membrane-associated proteins [PubMed1639195, PubMed14731533, PubMed7531822] for example, in a variety of proteins with enzymatic activity, in adaptor proteins that lack catalytic sequences and in cytoskeletal proteins, such as fodrin and yeast actin binding protein ABP-1.

The SH3 domain has a characteristic fold which consists of five or six beta-strands arranged as two tightly packed anti-parallel beta sheets. The linker regions may contain short helices. The surface of the SH2-domain bears a flat, hydrophobic ligand-binding pocket which consists of three shallow grooves defined by conservative aromatic residues in which the ligand adopts an extended left-handed helical arrangement. The ligand binds with low affinity but this may be enhanced by multiple interactions. The region bound by the SH3 domain is in all cases proline-rich and contains PXXP as a core-conserved binding motif. The function of the SH3 domain is not well understood but they may mediate many diverse processes such as increasing local concentration of proteins, altering their subcellular location and mediating the assembly of large multiprotein complexes [PubMed7953536].


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 · Enzyme Commission (EC) · Human Phenotype (HP) · Mouse Phenotype (MP) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Fly Phenotype (FP) · Fly Anatomy (FA) · Zebrafish Anatomy (ZA) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) ]

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 171 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 SH3-domain 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 171 hidden Markov models representing the SH3-domain 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 · Enzyme Commission (EC) · Human Phenotype (HP) · Mouse Phenotype (MP) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Fly Phenotype (FP) · Fly Anatomy (FA) · Zebrafish Anatomy (ZA) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · Internal database links ]