1OLZ
The ligand-binding face of the semaphorins revealed by the high resolution crystal structure of SEMA4D
External Resource: Annotation
Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage
Chains | Domain Info | Class | Fold | Superfamily | Family | Domain | Species | Provenance Source (Version) |
---|---|---|---|---|---|---|---|---|
A | d1olza1 | All beta proteins | Immunoglobulin-like beta-sandwich | Immunoglobulin | I set domains | Semaphorin 4d Ig-like domain | Human (Homo sapiens ) [TaxId: 9606 ], | SCOPe (2.08) |
A | d1olza2 | All beta proteins | 7-bladed beta-propeller | Sema domain | Sema domain | Semaphorin 4d | Human (Homo sapiens ) [TaxId: 9606 ], | SCOPe (2.08) |
A | d1olza3 | Small proteins | Trefoil/Plexin domain-like | Plexin repeat | Plexin repeat | Semaphorin 4d | Human (Homo sapiens ) [TaxId: 9606 ], | SCOPe (2.08) |
B | d1olzb1 | All beta proteins | Immunoglobulin-like beta-sandwich | Immunoglobulin | I set domains | Semaphorin 4d Ig-like domain | Human (Homo sapiens ) [TaxId: 9606 ], | SCOPe (2.08) |
B | d1olzb2 | All beta proteins | 7-bladed beta-propeller | Sema domain | Sema domain | Semaphorin 4d | Human (Homo sapiens ) [TaxId: 9606 ], | SCOPe (2.08) |
B | d1olzb3 | Small proteins | Trefoil/Plexin domain-like | Plexin repeat | Plexin repeat | Semaphorin 4d | 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 | SCOP2 Family | Sema domain-like | 8025262 | 4000934 | SCOP2 (2022-06-29) |
A | SCOP2 Family | Plexin repeat-like | 8025264 | 4001807 | SCOP2 (2022-06-29) |
A | SCOP2 Family | I set domains | 8054792 | 4007543 | SCOP2 (2022-06-29) |
A | SCOP2 Superfamily | Sema domain-like | 8037641 | 3000180 | SCOP2 (2022-06-29) |
A | SCOP2 Superfamily | Plexin repeat-like | 8037643 | 3000415 | SCOP2 (2022-06-29) |
A | SCOP2 Superfamily | Immunoglobulin (Ig) domain-like | 8054793 | 3000071 | SCOP2 (2022-06-29) |
B | SCOP2B Superfamily | Immunoglobulin (Ig) domain-like | 8054793 | 3000071 | SCOP2B (2022-06-29) |
B | SCOP2B Superfamily | Plexin repeat-like | 8037643 | 3000415 | SCOP2B (2022-06-29) |
B | SCOP2B Superfamily | Sema domain-like | 8037641 | 3000180 | 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 | I-set_3 | e1olzA1 | A: beta sandwiches | X: Immunoglobulin-like beta-sandwich | H: Immunoglobulin-related | T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like | F: I-set_3 | ECOD (1.6) |
A | Sema | e1olzA2 | A: beta duplicates or obligate multimers | X: beta-propeller-like | H: beta-propeller | T: 7-bladed | F: Sema | ECOD (1.6) |
A | PSI_1 | e1olzA3 | A: few secondary structure elements | X: Trefoil/Plexin domain-like (From Topology) | H: Trefoil/Plexin domain-like (From Topology) | T: Trefoil/Plexin domain-like | F: PSI_1 | ECOD (1.6) |
B | I-set_3 | e1olzB1 | A: beta sandwiches | X: Immunoglobulin-like beta-sandwich | H: Immunoglobulin-related | T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like | F: I-set_3 | ECOD (1.6) |
B | Sema | e1olzB2 | A: beta duplicates or obligate multimers | X: beta-propeller-like | H: beta-propeller | T: 7-bladed | F: Sema | ECOD (1.6) |
B | PSI_1 | e1olzB3 | A: few secondary structure elements | X: Trefoil/Plexin domain-like (From Topology) | H: Trefoil/Plexin domain-like (From Topology) | T: Trefoil/Plexin domain-like | F: PSI_1 | ECOD (1.6) |
Domain Annotation: CATH CATH Database Homepage
Chain | Domain | Class | Architecture | Topology | Homology | Provenance Source (Version) |
---|---|---|---|---|---|---|
A | 2.130.10.10 | Mainly Beta | 7 Propeller | Methylamine Dehydrogenase | Chain H | CATH (4.3.0) |
A | 3.30.1680.10 | Alpha Beta | 2-Layer Sandwich | ligand-binding face of the semaphorins, domain 2 | ligand-binding face of the semaphorins, domain 2 | CATH (4.3.0) |
A | 2.60.40.10 | Mainly Beta | Sandwich | Immunoglobulin-like | Immunoglobulins | CATH (4.3.0) |
B | 2.130.10.10 | Mainly Beta | 7 Propeller | Methylamine Dehydrogenase | Chain H | CATH (4.3.0) |
B | 3.30.1680.10 | Alpha Beta | 2-Layer Sandwich | ligand-binding face of the semaphorins, domain 2 | ligand-binding face of the semaphorins, domain 2 | CATH (4.3.0) |
B | 2.60.40.10 | Mainly Beta | Sandwich | Immunoglobulin-like | Immunoglobulins | CATH (4.3.0) |
Protein Family Annotation Pfam Database Homepage
Chains | Accession | Name | Description | Comments | Source |
---|---|---|---|---|---|
PF01437 | Plexin repeat (PSI) | Plexin repeat | - | Family | |
PF01403 | Sema domain (Sema) | Sema domain | - | Repeat | |
PF00047 | Immunoglobulin domain (ig) | Immunoglobulin domain | Members of the immunoglobulin superfamily are found in hundreds of proteins of different functions. Examples include antibodies, the giant muscle kinase titin and receptor tyrosine kinases. Immunoglobulin-like domains may be involved in protein-prote ... | Domain |
Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage
InterPro: Protein Family Classification InterPro Database Homepage
Chains | Accession | Name | Type |
---|---|---|---|
IPR036179 | Immunoglobulin-like domain superfamily | Homologous Superfamily | |
IPR003599 | Immunoglobulin domain subtype | Domain | |
IPR013151 | Immunoglobulin-like beta-sandwich domain | Domain | |
IPR013783 | Immunoglobulin-like fold | Homologous Superfamily | |
IPR036352 | Sema domain superfamily | Homologous Superfamily | |
IPR007110 | Immunoglobulin-like domain | Domain | |
IPR003598 | Immunoglobulin subtype 2 | Domain | |
IPR016201 | PSI domain | Domain | |
IPR027231 | Semaphorin | Family | |
IPR015943 | WD40/YVTN repeat-like-containing domain superfamily | Homologous Superfamily | |
IPR002165 | Plexin repeat | Repeat | |
IPR001627 | Sema domain | Domain |