1E6J
Crystal structure of HIV-1 capsid protein (p24) in complex with Fab13B5
Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage
Domain Annotation: ECOD Classification ECOD Database Homepage
Chains | Family Name | Domain Identifier | Architecture | Possible Homology | Homology | Topology | Family | Provenance Source (Version) |
---|---|---|---|---|---|---|---|---|
A [auth H] | C1-set_1 | e1e6jH2 | 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) |
A [auth H] | V-set_10 | e1e6jH1 | A: beta sandwiches | X: Immunoglobulin-like beta-sandwich | H: Immunoglobulin-related | T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like | F: V-set_10 | ECOD (1.6) |
B [auth L] | C1-set_4 | e1e6jL2 | A: beta sandwiches | X: Immunoglobulin-like beta-sandwich | H: Immunoglobulin-related | T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like | F: C1-set_4 | ECOD (1.6) |
B [auth L] | V-set | e1e6jL1 | 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) |
C [auth P] | Gag_p24_C | e1e6jP1 | A: alpha bundles | X: Retrovirus capsid protein | H: Retrovirus capsid protein-C (From Topology) | T: Retrovirus capsid protein-C | F: Gag_p24_C | ECOD (1.6) |
C [auth P] | Gag_p24_N | e1e6jP2 | A: alpha bundles | X: Retrovirus capsid protein | H: Retrovirus capsid protein N-terminal domain (From Topology) | T: Retrovirus capsid protein N-terminal domain | F: Gag_p24_N | ECOD (1.6) |
Domain Annotation: CATH CATH Database Homepage
Chain | Domain | Class | Architecture | Topology | Homology | Provenance Source (Version) |
---|---|---|---|---|---|---|
A [auth H] | 2.60.40.10 | Mainly Beta | Sandwich | Immunoglobulin-like | Immunoglobulins | CATH (4.3.0) |
B [auth L] | 2.60.40.10 | Mainly Beta | Sandwich | Immunoglobulin-like | Immunoglobulins | CATH (4.3.0) |
C [auth P] | 1.10.375.10 | Mainly Alpha | Orthogonal Bundle | Human Immunodeficiency Virus Type 1 Capsid Protein | Human Immunodeficiency Virus Type 1 Capsid Protein | CATH (4.3.0) |
C [auth P] | 1.10.1200.30 | Mainly Alpha | Orthogonal Bundle | Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein | Chain A | 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 H] | 13B5 mAb, anti-p24 [HIV-1] | VH-CH1 | Mus musculus (house mouse) | IGHV1-4*01, IGHJ2*01, IGHG1*02 | V-DOMAIN VH, C-DOMAIN CH1 | IG | FAB-GAMMA-1_KAPPA | IMGT (202443-0) |
B [auth L] | 13B5 mAb, anti-p24 [HIV-1] | L-KAPPA | Mus musculus (house mouse) | IGKV4-86*01, IGKJ2*03, IGKJ4*01, IGKC*01, IGKC*02 | V-DOMAIN V-KAPPA, C-DOMAIN C-KAPPA | IG | FAB-GAMMA-1_KAPPA | IMGT (202443-0) |
SAbDab Antibody Annotation SAbDab Database Homepage
Chain | Chain Class | Chain Subclass | Chain Type | Antigen Name(s) | Provenance Source |
---|---|---|---|---|---|
A [auth H] | Heavy Chain | IGHV1 | - | capsid protein p24 | SAbDab (2024-11-01) |
B [auth L] | Light Chain | IGKV4 | Kappa | capsid protein p24 | SAbDab (2024-11-01) |
Protein Family Annotation Pfam Database Homepage
Chains | Accession | Name | Description | Comments | Source |
---|---|---|---|---|---|
A [auth H] | PF07686 | Immunoglobulin V-set domain (V-set) | Immunoglobulin V-set domain | This domain is found in antibodies as well as neural protein P0 and CTL4 amongst others. | Domain |
A [auth H] | PF07654 | Immunoglobulin C1-set domain (C1-set) | Immunoglobulin C1-set domain | - | Domain |
C [auth P] | PF00607 | gag protein p24 N-terminal domain (Gag_p24) | gag protein p24 N-terminal domain | p24 forms inner protein layer of the nucleocapsid. ELISA tests for p24 is the most commonly used method to demonstrate virus replication both in vivo and in vitro. | Domain |
C [auth P] | PF19317 | Gag protein p24 C-terminal domain (Gag_p24_C) | Gag protein p24 C-terminal domain | p24 forms inner protein layer of the nucleocapsid. ELISA tests for p24 is the most commonly used method to demonstrate virus replication both in vivo and in vitro. | Domain |
Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage
Chains | Polymer | Molecular Function | Biological Process | Cellular Component |
---|---|---|---|---|
A [auth H] | IMMUNOGLOBULIN | - | - | |
B [auth L] | IMMUNOGLOBULIN | - | - | - |
C [auth P] | CAPSID PROTEIN P24 | - |
InterPro: Protein Family Classification InterPro Database Homepage
Chains | Accession | Name | Type |
---|---|---|---|
A [auth H] | IPR003597 | Immunoglobulin C1-set | Domain |
A [auth H] | IPR013783 | Immunoglobulin-like fold | Homologous Superfamily |
A [auth H] | IPR036179 | Immunoglobulin-like domain superfamily | Homologous Superfamily |
A [auth H] | IPR013106 | Immunoglobulin V-set domain | Domain |
A [auth H] | IPR003599 | Immunoglobulin domain subtype | Domain |
A [auth H] | IPR007110 | Immunoglobulin-like domain | Domain |
A [auth H] | IPR050380 | Immune Recognition and Response Modulators | Family |
C [auth P] | IPR045345 | Retroviral nucleocapsid Gag protein p24, C-terminal domain | Domain |
C [auth P] | IPR008919 | Retrovirus capsid, N-terminal | Homologous Superfamily |
C [auth P] | IPR050195 | Primate lentivirus group Gag polyprotein-like | Domain |
C [auth P] | IPR008916 | Retrovirus capsid, C-terminal | Homologous Superfamily |