3VRL

Crystal structure of BMJ4 p24 capsid protein in complex with A10F9 Fab

External Resource: Annotation


Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

ChainsTypeFamily Name Domain Identifier Family IdentifierProvenance Source (Version)
CSCOP2 FamilyRetrovirus capsid protein C-terminal domain8077065 4000865 SCOP2 (2022-06-29)
CSCOP2 SuperfamilyRetrovirus capsid dimerization domain-like8077066 3001819 SCOP2 (2022-06-29)
F [auth D]SCOP2B SuperfamilyRetrovirus capsid dimerization domain-like8077066 3001819 SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

ChainsFamily NameDomain Identifier ArchitecturePossible HomologyHomologyTopologyFamilyProvenance Source (Version)
A [auth H]C1-set_1e3vrlH1 A: beta sandwichesX: Immunoglobulin-like beta-sandwichH: Immunoglobulin-relatedT: Immunoglobulin/Fibronectin type III/E set domains/PapD-likeF: C1-set_1ECOD (1.6)
A [auth H]V-set_12e3vrlH2 A: beta sandwichesX: Immunoglobulin-like beta-sandwichH: Immunoglobulin-relatedT: Immunoglobulin/Fibronectin type III/E set domains/PapD-likeF: V-set_12ECOD (1.6)
D [auth E]C1-set_1e3vrlE2 A: beta sandwichesX: Immunoglobulin-like beta-sandwichH: Immunoglobulin-relatedT: Immunoglobulin/Fibronectin type III/E set domains/PapD-likeF: C1-set_1ECOD (1.6)
D [auth E]V-set_12e3vrlE1 A: beta sandwichesX: Immunoglobulin-like beta-sandwichH: Immunoglobulin-relatedT: Immunoglobulin/Fibronectin type III/E set domains/PapD-likeF: V-set_12ECOD (1.6)
B [auth L]C1-set_4e3vrlL2 A: beta sandwichesX: Immunoglobulin-like beta-sandwichH: Immunoglobulin-relatedT: Immunoglobulin/Fibronectin type III/E set domains/PapD-likeF: C1-set_4ECOD (1.6)
B [auth L]V-sete3vrlL1 A: beta sandwichesX: Immunoglobulin-like beta-sandwichH: Immunoglobulin-relatedT: Immunoglobulin/Fibronectin type III/E set domains/PapD-likeF: V-setECOD (1.6)
E [auth F]C1-set_4e3vrlF2 A: beta sandwichesX: Immunoglobulin-like beta-sandwichH: Immunoglobulin-relatedT: Immunoglobulin/Fibronectin type III/E set domains/PapD-likeF: C1-set_4ECOD (1.6)
E [auth F]V-sete3vrlF1 A: beta sandwichesX: Immunoglobulin-like beta-sandwichH: Immunoglobulin-relatedT: Immunoglobulin/Fibronectin type III/E set domains/PapD-likeF: V-setECOD (1.6)
CGag_p24_Ce3vrlC1 A: alpha bundlesX: Retrovirus capsid proteinH: Retrovirus capsid protein-C (From Topology)T: Retrovirus capsid protein-CF: Gag_p24_CECOD (1.6)
F [auth D]Gag_p24_Ce3vrlD1 A: alpha bundlesX: Retrovirus capsid proteinH: Retrovirus capsid protein-C (From Topology)T: Retrovirus capsid protein-CF: Gag_p24_CECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

ChainDomainClassArchitectureTopologyHomologyProvenance Source (Version)
A [auth H]2.60.40.10 Mainly Beta Sandwich Immunoglobulin-like ImmunoglobulinsCATH (4.3.0)
D [auth E]2.60.40.10 Mainly Beta Sandwich Immunoglobulin-like ImmunoglobulinsCATH (4.3.0)
B [auth L]2.60.40.10 Mainly Beta Sandwich Immunoglobulin-like ImmunoglobulinsCATH (4.3.0)
E [auth F]2.60.40.10 Mainly Beta Sandwich Immunoglobulin-like ImmunoglobulinsCATH (4.3.0)
C1.10.1200.30 Mainly Alpha Orthogonal Bundle Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein Chain ACATH (4.3.0)
F [auth D]1.10.1200.30 Mainly Alpha Orthogonal Bundle Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein Chain ACATH (4.3.0)

IMGT Antibody Annotation IMGT Database Homepage

ChainProtein NameDescriptionOrganism NameGene Allele Name(s)Domain Name(s)Receptor TypeReceptor DescriptionProvenance Source
A [auth H],
D [auth E]		A10F9 Fab VH-CH1 Mus musculus (house mouse) IGHV5-6-4*01, IGHJ4*01, IGHG1*02 V-DOMAIN VH, C-DOMAIN CH1 IG FAB-GAMMA-1_KAPPA IMGT (202415-0)
B [auth L],
E [auth F]		A10F9 Fab L-KAPPA Mus musculus (house mouse) IGKV12-41*02, IGKV12-41*01, IGKJ1*01, IGKJ1*02, IGKJ2*01, IGKC*01, IGKC*02 V-DOMAIN V-KAPPA, C-DOMAIN C-KAPPA IG FAB-GAMMA-1_KAPPA IMGT (202415-0)

SAbDab Antibody Annotation SAbDab Database Homepage

ChainChain ClassChain SubclassChain TypeAntigen Name(s) Provenance Source
A [auth H],
D [auth E]		Heavy ChainIGHV5 -gag proteinSAbDab (2024-04-19)
B [auth L],
E [auth F]		Light ChainIGKV12 Kappagag proteinSAbDab (2024-04-19)

Protein Family Annotation Pfam Database Homepage

ChainsAccessionNameDescriptionCommentsSource
A [auth H],
D [auth E]		PF07686Immunoglobulin V-set domain (V-set)Immunoglobulin V-set domainThis domain is found in antibodies as well as neural protein P0 and CTL4 amongst others.Domain
A [auth H],
D [auth E]		PF07654Immunoglobulin C1-set domain (C1-set)Immunoglobulin C1-set domain- Domain
B [auth L],
E [auth F]		PF07686Immunoglobulin V-set domain (V-set)Immunoglobulin V-set domainThis domain is found in antibodies as well as neural protein P0 and CTL4 amongst others.Domain
B [auth L],
E [auth F]		PF07654Immunoglobulin C1-set domain (C1-set)Immunoglobulin C1-set domain- Domain
C,
F [auth D]		PF19317Gag protein p24 C-terminal domain (Gag_p24_C)Gag protein p24 C-terminal domainp24 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

ChainsPolymerMolecular FunctionBiological ProcessCellular Component
A [auth H],
D [auth E]		A10F9 Fab heavy chain-
B [auth L],
E [auth F]		A10F9 Fab light chain- - -
C,
F [auth D]		Gag protein

InterPro: Protein Family Classification InterPro Database Homepage

ChainsAccessionNameType
A [auth H],
D [auth E]		IPR003597Immunoglobulin C1-setDomain
A [auth H],
D [auth E]		IPR013783Immunoglobulin-like foldHomologous Superfamily
A [auth H],
D [auth E]		IPR036179Immunoglobulin-like domain superfamilyHomologous Superfamily
A [auth H],
D [auth E]		IPR003599Immunoglobulin subtypeDomain
A [auth H],
D [auth E]		IPR013106Immunoglobulin V-set domainDomain
A [auth H],
D [auth E]		IPR007110Immunoglobulin-like domainDomain
B [auth L],
E [auth F]		IPR003597Immunoglobulin C1-setDomain
B [auth L],
E [auth F]		IPR013783Immunoglobulin-like foldHomologous Superfamily
B [auth L],
E [auth F]		IPR036179Immunoglobulin-like domain superfamilyHomologous Superfamily
B [auth L],
E [auth F]		IPR003599Immunoglobulin subtypeDomain
B [auth L],
E [auth F]		IPR013106Immunoglobulin V-set domainDomain
B [auth L],
E [auth F]		IPR007110Immunoglobulin-like domainDomain
B [auth L],
E [auth F]		IPR003006Immunoglobulin/major histocompatibility complex, conserved siteConserved Site
C,
F [auth D]		IPR000071Immunodeficiency lentiviral matrix, N-terminalDomain
C,
F [auth D]		IPR045345Retroviral nucleocapsid Gag protein p24, C-terminal domainDomain
C,
F [auth D]		IPR036875Zinc finger, CCHC-type superfamilyHomologous Superfamily
C,
F [auth D]		IPR001878Zinc finger, CCHC-typeDomain
C,
F [auth D]		IPR008919Retrovirus capsid, N-terminalHomologous Superfamily
C,
F [auth D]		IPR010999Retroviral matrix proteinHomologous Superfamily
C,
F [auth D]		IPR012344Matrix protein, lentiviral and alpha-retroviral, N-terminalHomologous Superfamily
C,
F [auth D]		IPR014817Gag protein p6Domain
C,
F [auth D]		IPR008916Retrovirus capsid, C-terminalHomologous Superfamily