4JO1
Crystal structure of rabbit mAb R56 Fab in complex with V3 crown of HIV-1 JR-FL gp120
Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage
Chains | Domain Info | Class | Fold | Superfamily | Family | Domain | Species | Provenance Source (Version) |
---|---|---|---|---|---|---|---|---|
A [auth L] | d4jo1l1 | All beta proteins | Immunoglobulin-like beta-sandwich | Immunoglobulin | automated matches | automated matches | rabbit (Oryctolagus cuniculus ) [TaxId: 9986 ], | SCOPe (2.08) |
D [auth M] | d4jo1m1 | All beta proteins | Immunoglobulin-like beta-sandwich | Immunoglobulin | automated matches | automated matches | rabbit (Oryctolagus cuniculus ) [TaxId: 9986 ], | SCOPe (2.08) |
B [auth H] | d4jo1h_ | All beta proteins | Immunoglobulin-like beta-sandwich | Immunoglobulin | automated matches | automated matches | rabbit (Oryctolagus cuniculus ) [TaxId: 9986 ], | SCOPe (2.08) |
E [auth I] | d4jo1i_ | All beta proteins | Immunoglobulin-like beta-sandwich | Immunoglobulin | automated matches | automated matches | rabbit (Oryctolagus cuniculus ) [TaxId: 9986 ], | SCOPe (2.08) |
Domain Annotation: ECOD Classification ECOD Database Homepage
Chains | Family Name | Domain Identifier | Architecture | Possible Homology | Homology | Topology | Family | Provenance Source (Version) |
---|---|---|---|---|---|---|---|---|
A [auth L] | C1-set | e4jo1L1 | A: beta sandwiches | X: Immunoglobulin-like beta-sandwich | H: Immunoglobulin-related | T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like | F: C1-set | ECOD (1.6) |
A [auth L] | V-set | e4jo1L2 | A: beta sandwiches | X: Immunoglobulin-like beta-sandwich | H: Immunoglobulin-related | T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like | F: V-set | ECOD (1.6) |
D [auth M] | C1-set | e4jo1M1 | A: beta sandwiches | X: Immunoglobulin-like beta-sandwich | H: Immunoglobulin-related | T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like | F: C1-set | ECOD (1.6) |
D [auth M] | V-set | e4jo1M2 | A: beta sandwiches | X: Immunoglobulin-like beta-sandwich | H: Immunoglobulin-related | T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like | F: V-set | ECOD (1.6) |
B [auth H] | C1-set_1 | e4jo1H1 | A: beta sandwiches | X: Immunoglobulin-like beta-sandwich | H: Immunoglobulin-related | T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like | F: C1-set_1 | ECOD (1.6) |
B [auth H] | V-set_12 | e4jo1H2 | A: beta sandwiches | X: Immunoglobulin-like beta-sandwich | H: Immunoglobulin-related | T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like | F: V-set_12 | ECOD (1.6) |
E [auth I] | C1-set_1 | e4jo1I1 | A: beta sandwiches | X: Immunoglobulin-like beta-sandwich | H: Immunoglobulin-related | T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like | F: C1-set_1 | ECOD (1.6) |
E [auth I] | V-set_12 | e4jo1I2 | A: beta sandwiches | X: Immunoglobulin-like beta-sandwich | H: Immunoglobulin-related | T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like | F: V-set_12 | ECOD (1.6) |
Domain Annotation: CATH CATH Database Homepage
Chain | Domain | Class | Architecture | Topology | Homology | Provenance Source (Version) |
---|---|---|---|---|---|---|
A [auth L] | 2.60.40.10 | Mainly Beta | Sandwich | Immunoglobulin-like | Immunoglobulins | CATH (4.3.0) |
D [auth M] | 2.60.40.10 | Mainly Beta | Sandwich | Immunoglobulin-like | Immunoglobulins | CATH (4.3.0) |
B [auth H] | 2.60.40.10 | Mainly Beta | Sandwich | Immunoglobulin-like | Immunoglobulins | CATH (4.3.0) |
E [auth I] | 2.60.40.10 | Mainly Beta | Sandwich | Immunoglobulin-like | Immunoglobulins | CATH (4.3.0) |
IMGT Antibody Annotation IMGT Database Homepage
Chain | Protein Name | Description | Organism Name | Gene Allele Name(s) | Domain Name(s) | Receptor Type | Receptor Description | Provenance Source |
---|---|---|---|---|---|---|---|---|
A [auth L], D [auth M] | R56 Fab, anti-gp120 [HIV-1] | L-KAPPA | Oryctolagus cuniculus (rabbit) | IGKV1S5*01, IGKJ1-2*02, IGKJ1-2*01, IGKC1*01 | V-DOMAIN V-KAPPA, C-DOMAIN C-KAPPA | IG | FAB-GAMMA-1_KAPPA | IMGT (202432-0) |
B [auth H], E [auth I] | R56 Fab, anti-gp120 [HIV-1] | VH-CH1 | Oryctolagus cuniculus (rabbit) | IGHV1S40*01, IGHJ6*01, IGHG*01, IGHG*05, IGHG*02 | V-DOMAIN VH, C-DOMAIN CH1 | IG | FAB-GAMMA-1_KAPPA | IMGT (202432-0) |
SAbDab Antibody Annotation SAbDab Database Homepage
Chain | Chain Class | Chain Subclass | Chain Type | Antigen Name(s) | Provenance Source |
---|---|---|---|---|---|
A [auth L], D [auth M] | Light Chain | IGKV1 | Kappa | gp120 | SAbDab (2024-08-16) |
B [auth H], E [auth I] | Heavy Chain | IGHV1 | - | gp120 | SAbDab (2024-08-16) |
Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage
Chains | Polymer | Molecular Function | Biological Process | Cellular Component |
---|---|---|---|---|
A [auth L], D [auth M] | monoclonal anti-HIV-1 gp120 V3 antibody R56 light chain | - | - | - |
B [auth H], E [auth I] | monoclonal anti-HIV-1 gp120 V3 antibody R56 heavy chain | - | - | - |
C [auth P], F [auth Q] | gp120 | - | - |
InterPro: Protein Family Classification InterPro Database Homepage
Chains | Accession | Name | Type |
---|---|---|---|
C [auth P], F [auth Q] | IPR000777 | Human immunodeficiency virus 1, envelope glycoprotein Gp120 | Domain |
C [auth P], F [auth Q] | IPR036377 | Gp120 core superfamily | Homologous Superfamily |