Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

ChainsDomain InfoClassFoldSuperfamilyFamilyDomainSpeciesProvenance Source (Version)
Ad4wyma2 All alpha proteins Acyl carrier protein-like Retrovirus capsid dimerization domain-like automated matches automated matches HIV-1 (Human immunodeficiency virus type 1 (NEW YORK-5 ISOLATE) ) [TaxId: 11698 ], SCOPe (2.08)
Ad4wyma1 All alpha proteins Retrovirus capsid protein, N-terminal core domain Retrovirus capsid protein, N-terminal core domain Retrovirus capsid protein, N-terminal core domain HIV-1 capsid protein HIV-1 (Human immunodeficiency virus type 1 (NEW YORK-5 ISOLATE) ) [TaxId: 11698 ], SCOPe (2.08)
Bd4wymb2 All alpha proteins Acyl carrier protein-like Retrovirus capsid dimerization domain-like automated matches automated matches HIV-1 (Human immunodeficiency virus type 1 (NEW YORK-5 ISOLATE) ) [TaxId: 11698 ], SCOPe (2.08)
Bd4wymb1 All alpha proteins Retrovirus capsid protein, N-terminal core domain Retrovirus capsid protein, N-terminal core domain Retrovirus capsid protein, N-terminal core domain HIV-1 capsid protein HIV-1 (Human immunodeficiency virus type 1 (NEW YORK-5 ISOLATE) ) [TaxId: 11698 ], SCOPe (2.08)
Cd4wymc2 All alpha proteins Acyl carrier protein-like Retrovirus capsid dimerization domain-like automated matches automated matches HIV-1 (Human immunodeficiency virus type 1 (NEW YORK-5 ISOLATE) ) [TaxId: 11698 ], SCOPe (2.08)
Cd4wymc1 All alpha proteins Retrovirus capsid protein, N-terminal core domain Retrovirus capsid protein, N-terminal core domain Retrovirus capsid protein, N-terminal core domain HIV-1 capsid protein HIV-1 (Human immunodeficiency virus type 1 (NEW YORK-5 ISOLATE) ) [TaxId: 11698 ], SCOPe (2.08)
Dd4wymd2 All alpha proteins Acyl carrier protein-like Retrovirus capsid dimerization domain-like automated matches automated matches HIV-1 (Human immunodeficiency virus type 1 (NEW YORK-5 ISOLATE) ) [TaxId: 11698 ], SCOPe (2.08)
Dd4wymd1 All alpha proteins Retrovirus capsid protein, N-terminal core domain Retrovirus capsid protein, N-terminal core domain Retrovirus capsid protein, N-terminal core domain HIV-1 capsid protein HIV-1 (Human immunodeficiency virus type 1 (NEW YORK-5 ISOLATE) ) [TaxId: 11698 ], SCOPe (2.08)
Ed4wyme2 All alpha proteins Acyl carrier protein-like Retrovirus capsid dimerization domain-like automated matches automated matches HIV-1 (Human immunodeficiency virus type 1 (NEW YORK-5 ISOLATE) ) [TaxId: 11698 ], SCOPe (2.08)
Ed4wyme1 All alpha proteins Retrovirus capsid protein, N-terminal core domain Retrovirus capsid protein, N-terminal core domain Retrovirus capsid protein, N-terminal core domain HIV-1 capsid protein HIV-1 (Human immunodeficiency virus type 1 (NEW YORK-5 ISOLATE) ) [TaxId: 11698 ], SCOPe (2.08)
Fd4wymf2 All alpha proteins Acyl carrier protein-like Retrovirus capsid dimerization domain-like automated matches automated matches HIV-1 (Human immunodeficiency virus type 1 (NEW YORK-5 ISOLATE) ) [TaxId: 11698 ], SCOPe (2.08)
Fd4wymf1 All alpha proteins Retrovirus capsid protein, N-terminal core domain Retrovirus capsid protein, N-terminal core domain Retrovirus capsid protein, N-terminal core domain HIV-1 capsid protein HIV-1 (Human immunodeficiency virus type 1 (NEW YORK-5 ISOLATE) ) [TaxId: 11698 ], SCOPe (2.08)
Gd4wymg2 All alpha proteins Acyl carrier protein-like Retrovirus capsid dimerization domain-like automated matches automated matches HIV-1 (Human immunodeficiency virus type 1 (NEW YORK-5 ISOLATE) ) [TaxId: 11698 ], SCOPe (2.08)
Gd4wymg1 All alpha proteins Retrovirus capsid protein, N-terminal core domain Retrovirus capsid protein, N-terminal core domain Retrovirus capsid protein, N-terminal core domain HIV-1 capsid protein HIV-1 (Human immunodeficiency virus type 1 (NEW YORK-5 ISOLATE) ) [TaxId: 11698 ], SCOPe (2.08)
Hd4wymh2 All alpha proteins Acyl carrier protein-like Retrovirus capsid dimerization domain-like automated matches automated matches HIV-1 (Human immunodeficiency virus type 1 (NEW YORK-5 ISOLATE) ) [TaxId: 11698 ], SCOPe (2.08)
Hd4wymh1 All alpha proteins Retrovirus capsid protein, N-terminal core domain Retrovirus capsid protein, N-terminal core domain Retrovirus capsid protein, N-terminal core domain HIV-1 capsid protein HIV-1 (Human immunodeficiency virus type 1 (NEW YORK-5 ISOLATE) ) [TaxId: 11698 ], SCOPe (2.08)
Id4wymi1 All alpha proteins Retrovirus capsid protein, N-terminal core domain Retrovirus capsid protein, N-terminal core domain Retrovirus capsid protein, N-terminal core domain HIV-1 capsid protein HIV-1 (Human immunodeficiency virus type 1 (NEW YORK-5 ISOLATE) ) [TaxId: 11698 ], SCOPe (2.08)
Jd4wymj2 All alpha proteins Acyl carrier protein-like Retrovirus capsid dimerization domain-like automated matches automated matches HIV-1 (Human immunodeficiency virus type 1 (NEW YORK-5 ISOLATE) ) [TaxId: 11698 ], SCOPe (2.08)
Jd4wymj1 All alpha proteins Retrovirus capsid protein, N-terminal core domain Retrovirus capsid protein, N-terminal core domain Retrovirus capsid protein, N-terminal core domain HIV-1 capsid protein HIV-1 (Human immunodeficiency virus type 1 (NEW YORK-5 ISOLATE) ) [TaxId: 11698 ], SCOPe (2.08)
Kd4wymk2 All alpha proteins Acyl carrier protein-like Retrovirus capsid dimerization domain-like automated matches automated matches HIV-1 (Human immunodeficiency virus type 1 (NEW YORK-5 ISOLATE) ) [TaxId: 11698 ], SCOPe (2.08)
Kd4wymk1 All alpha proteins Retrovirus capsid protein, N-terminal core domain Retrovirus capsid protein, N-terminal core domain Retrovirus capsid protein, N-terminal core domain HIV-1 capsid protein HIV-1 (Human immunodeficiency virus type 1 (NEW YORK-5 ISOLATE) ) [TaxId: 11698 ], SCOPe (2.08)
Ld4wyml1 All alpha proteins Retrovirus capsid protein, N-terminal core domain Retrovirus capsid protein, N-terminal core domain Retrovirus capsid protein, N-terminal core domain HIV-1 capsid protein HIV-1 (Human immunodeficiency virus type 1 (NEW YORK-5 ISOLATE) ) [TaxId: 11698 ], SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

ChainsTypeFamily Name Domain Identifier Family IdentifierProvenance Source (Version)
ASCOP2B SuperfamilyRetrovirus capsid dimerization domain-like 8077054 3001819 SCOP2B (2022-06-29)
BSCOP2B SuperfamilyRetrovirus capsid dimerization domain-like 8077054 3001819 SCOP2B (2022-06-29)
CSCOP2B SuperfamilyRetrovirus capsid dimerization domain-like 8077054 3001819 SCOP2B (2022-06-29)
DSCOP2B SuperfamilyRetrovirus capsid dimerization domain-like 8077054 3001819 SCOP2B (2022-06-29)
ESCOP2B SuperfamilyRetrovirus capsid dimerization domain-like 8077054 3001819 SCOP2B (2022-06-29)
FSCOP2B SuperfamilyRetrovirus capsid dimerization domain-like 8077054 3001819 SCOP2B (2022-06-29)
GSCOP2B SuperfamilyRetrovirus capsid dimerization domain-like 8077054 3001819 SCOP2B (2022-06-29)
HSCOP2B SuperfamilyRetrovirus capsid dimerization domain-like 8077054 3001819 SCOP2B (2022-06-29)
ISCOP2B SuperfamilyRetrovirus capsid dimerization domain-like 8077054 3001819 SCOP2B (2022-06-29)
JSCOP2B SuperfamilyRetrovirus capsid dimerization domain-like 8077054 3001819 SCOP2B (2022-06-29)
KSCOP2B SuperfamilyRetrovirus capsid dimerization domain-like 8077054 3001819 SCOP2B (2022-06-29)
LSCOP2B SuperfamilyRetrovirus capsid dimerization domain-like 8077054 3001819 SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

ChainsFamily NameDomain Identifier ArchitecturePossible HomologyHomologyTopologyFamilyProvenance Source (Version)
AGag_p24_Ce4wymA1 A: alpha bundlesX: Retrovirus capsid proteinH: Retrovirus capsid protein-C (From Topology)T: Retrovirus capsid protein-CF: Gag_p24_CECOD (1.6)
AGag_p24_Ne4wymA2 A: alpha bundlesX: Retrovirus capsid proteinH: Retrovirus capsid protein N-terminal domain (From Topology)T: Retrovirus capsid protein N-terminal domainF: Gag_p24_NECOD (1.6)
BGag_p24_Ce4wymB2 A: alpha bundlesX: Retrovirus capsid proteinH: Retrovirus capsid protein-C (From Topology)T: Retrovirus capsid protein-CF: Gag_p24_CECOD (1.6)
BGag_p24_Ne4wymB1 A: alpha bundlesX: Retrovirus capsid proteinH: Retrovirus capsid protein N-terminal domain (From Topology)T: Retrovirus capsid protein N-terminal domainF: Gag_p24_NECOD (1.6)
CGag_p24_Ce4wymC2 A: alpha bundlesX: Retrovirus capsid proteinH: Retrovirus capsid protein-C (From Topology)T: Retrovirus capsid protein-CF: Gag_p24_CECOD (1.6)
CGag_p24_Ne4wymC1 A: alpha bundlesX: Retrovirus capsid proteinH: Retrovirus capsid protein N-terminal domain (From Topology)T: Retrovirus capsid protein N-terminal domainF: Gag_p24_NECOD (1.6)
DGag_p24_Ce4wymD2 A: alpha bundlesX: Retrovirus capsid proteinH: Retrovirus capsid protein-C (From Topology)T: Retrovirus capsid protein-CF: Gag_p24_CECOD (1.6)
DGag_p24_Ne4wymD1 A: alpha bundlesX: Retrovirus capsid proteinH: Retrovirus capsid protein N-terminal domain (From Topology)T: Retrovirus capsid protein N-terminal domainF: Gag_p24_NECOD (1.6)
EGag_p24_Ce4wymE2 A: alpha bundlesX: Retrovirus capsid proteinH: Retrovirus capsid protein-C (From Topology)T: Retrovirus capsid protein-CF: Gag_p24_CECOD (1.6)
EGag_p24_Ne4wymE1 A: alpha bundlesX: Retrovirus capsid proteinH: Retrovirus capsid protein N-terminal domain (From Topology)T: Retrovirus capsid protein N-terminal domainF: Gag_p24_NECOD (1.6)
FGag_p24_Ce4wymF2 A: alpha bundlesX: Retrovirus capsid proteinH: Retrovirus capsid protein-C (From Topology)T: Retrovirus capsid protein-CF: Gag_p24_CECOD (1.6)
FGag_p24_Ne4wymF1 A: alpha bundlesX: Retrovirus capsid proteinH: Retrovirus capsid protein N-terminal domain (From Topology)T: Retrovirus capsid protein N-terminal domainF: Gag_p24_NECOD (1.6)
GGag_p24_Ce4wymG2 A: alpha bundlesX: Retrovirus capsid proteinH: Retrovirus capsid protein-C (From Topology)T: Retrovirus capsid protein-CF: Gag_p24_CECOD (1.6)
GGag_p24_Ne4wymG1 A: alpha bundlesX: Retrovirus capsid proteinH: Retrovirus capsid protein N-terminal domain (From Topology)T: Retrovirus capsid protein N-terminal domainF: Gag_p24_NECOD (1.6)
HGag_p24_Ce4wymH2 A: alpha bundlesX: Retrovirus capsid proteinH: Retrovirus capsid protein-C (From Topology)T: Retrovirus capsid protein-CF: Gag_p24_CECOD (1.6)
HGag_p24_Ne4wymH1 A: alpha bundlesX: Retrovirus capsid proteinH: Retrovirus capsid protein N-terminal domain (From Topology)T: Retrovirus capsid protein N-terminal domainF: Gag_p24_NECOD (1.6)
IGag_p24_Ce4wymI2 A: alpha bundlesX: Retrovirus capsid proteinH: Retrovirus capsid protein-C (From Topology)T: Retrovirus capsid protein-CF: Gag_p24_CECOD (1.6)
IGag_p24_Ne4wymI1 A: alpha bundlesX: Retrovirus capsid proteinH: Retrovirus capsid protein N-terminal domain (From Topology)T: Retrovirus capsid protein N-terminal domainF: Gag_p24_NECOD (1.6)
JGag_p24_Ce4wymJ2 A: alpha bundlesX: Retrovirus capsid proteinH: Retrovirus capsid protein-C (From Topology)T: Retrovirus capsid protein-CF: Gag_p24_CECOD (1.6)
JGag_p24_Ne4wymJ1 A: alpha bundlesX: Retrovirus capsid proteinH: Retrovirus capsid protein N-terminal domain (From Topology)T: Retrovirus capsid protein N-terminal domainF: Gag_p24_NECOD (1.6)
KGag_p24_Ce4wymK2 A: alpha bundlesX: Retrovirus capsid proteinH: Retrovirus capsid protein-C (From Topology)T: Retrovirus capsid protein-CF: Gag_p24_CECOD (1.6)
KGag_p24_Ne4wymK1 A: alpha bundlesX: Retrovirus capsid proteinH: Retrovirus capsid protein N-terminal domain (From Topology)T: Retrovirus capsid protein N-terminal domainF: Gag_p24_NECOD (1.6)
LGag_p24_Ce4wymL2 A: alpha bundlesX: Retrovirus capsid proteinH: Retrovirus capsid protein-C (From Topology)T: Retrovirus capsid protein-CF: Gag_p24_CECOD (1.6)
LGag_p24_Ne4wymL1 A: alpha bundlesX: Retrovirus capsid proteinH: Retrovirus capsid protein N-terminal domain (From Topology)T: Retrovirus capsid protein N-terminal domainF: Gag_p24_NECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

ChainDomainClassArchitectureTopologyHomologyProvenance Source (Version)
A1.10.375.10 Mainly Alpha Orthogonal Bundle Human Immunodeficiency Virus Type 1 Capsid Protein Human Immunodeficiency Virus Type 1 Capsid ProteinCATH (4.3.0)
A1.10.1200.30 Mainly Alpha Orthogonal Bundle Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein Chain ACATH (4.3.0)
B1.10.375.10 Mainly Alpha Orthogonal Bundle Human Immunodeficiency Virus Type 1 Capsid Protein Human Immunodeficiency Virus Type 1 Capsid ProteinCATH (4.3.0)
B1.10.1200.30 Mainly Alpha Orthogonal Bundle Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein Chain ACATH (4.3.0)
C1.10.375.10 Mainly Alpha Orthogonal Bundle Human Immunodeficiency Virus Type 1 Capsid Protein Human Immunodeficiency Virus Type 1 Capsid ProteinCATH (4.3.0)
C1.10.1200.30 Mainly Alpha Orthogonal Bundle Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein Chain ACATH (4.3.0)
D1.10.375.10 Mainly Alpha Orthogonal Bundle Human Immunodeficiency Virus Type 1 Capsid Protein Human Immunodeficiency Virus Type 1 Capsid ProteinCATH (4.3.0)
D1.10.1200.30 Mainly Alpha Orthogonal Bundle Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein Chain ACATH (4.3.0)
E1.10.375.10 Mainly Alpha Orthogonal Bundle Human Immunodeficiency Virus Type 1 Capsid Protein Human Immunodeficiency Virus Type 1 Capsid ProteinCATH (4.3.0)
E1.10.1200.30 Mainly Alpha Orthogonal Bundle Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein Chain ACATH (4.3.0)
F1.10.375.10 Mainly Alpha Orthogonal Bundle Human Immunodeficiency Virus Type 1 Capsid Protein Human Immunodeficiency Virus Type 1 Capsid ProteinCATH (4.3.0)
F1.10.1200.30 Mainly Alpha Orthogonal Bundle Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein Chain ACATH (4.3.0)
G1.10.375.10 Mainly Alpha Orthogonal Bundle Human Immunodeficiency Virus Type 1 Capsid Protein Human Immunodeficiency Virus Type 1 Capsid ProteinCATH (4.3.0)
G1.10.1200.30 Mainly Alpha Orthogonal Bundle Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein Chain ACATH (4.3.0)
H1.10.375.10 Mainly Alpha Orthogonal Bundle Human Immunodeficiency Virus Type 1 Capsid Protein Human Immunodeficiency Virus Type 1 Capsid ProteinCATH (4.3.0)
H1.10.1200.30 Mainly Alpha Orthogonal Bundle Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein Chain ACATH (4.3.0)
I1.10.375.10 Mainly Alpha Orthogonal Bundle Human Immunodeficiency Virus Type 1 Capsid Protein Human Immunodeficiency Virus Type 1 Capsid ProteinCATH (4.3.0)
I1.10.1200.30 Mainly Alpha Orthogonal Bundle Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein Chain ACATH (4.3.0)
J1.10.375.10 Mainly Alpha Orthogonal Bundle Human Immunodeficiency Virus Type 1 Capsid Protein Human Immunodeficiency Virus Type 1 Capsid ProteinCATH (4.3.0)
J1.10.1200.30 Mainly Alpha Orthogonal Bundle Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein Chain ACATH (4.3.0)
K1.10.375.10 Mainly Alpha Orthogonal Bundle Human Immunodeficiency Virus Type 1 Capsid Protein Human Immunodeficiency Virus Type 1 Capsid ProteinCATH (4.3.0)
K1.10.1200.30 Mainly Alpha Orthogonal Bundle Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein Chain ACATH (4.3.0)
L1.10.375.10 Mainly Alpha Orthogonal Bundle Human Immunodeficiency Virus Type 1 Capsid Protein Human Immunodeficiency Virus Type 1 Capsid ProteinCATH (4.3.0)
L1.10.1200.30 Mainly Alpha Orthogonal Bundle Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein Chain ACATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

ChainsAccessionNameDescriptionCommentsSource
A, B, C, D, E
PF00607gag protein p24 N-terminal domain (Gag_p24)gag protein p24 N-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
A, B, C, D, E
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, B, C, D, E
Capsid protein p24
M, N, O, P, Q
ISOFORM 2 OF CLEAVAGE AND POLYADENYLATION SPECIFICITY FACTOR SUBUNIT 6

InterPro: Protein Family Classification InterPro Database Homepage

ChainsAccessionNameType
A, B, C, D, E
IPR000071Immunodeficiency lentiviral matrix, N-terminalDomain
A, B, C, D, E
IPR045345Retroviral nucleocapsid Gag protein p24, C-terminal domainDomain
A, B, C, D, E
IPR036875Zinc finger, CCHC-type superfamilyHomologous Superfamily
A, B, C, D, E
IPR050195Primate lentivirus group Gag polyprotein-likeDomain
A, B, C, D, E
IPR001878Zinc finger, CCHC-typeDomain
A, B, C, D, E
IPR008919Retrovirus capsid, N-terminalHomologous Superfamily
A, B, C, D, E
IPR010999Retroviral matrix proteinHomologous Superfamily
A, B, C, D, E
IPR012344Matrix protein, lentiviral and alpha-retroviral, N-terminalHomologous Superfamily
A, B, C, D, E
IPR014817Gag protein p6Domain
A, B, C, D, E
IPR008916Retrovirus capsid, C-terminalHomologous Superfamily
M, N, O, P, Q
IPR034772CPSF6/7 familyFamily
M, N, O, P, Q
IPR000504RNA recognition motif domainDomain
M, N, O, P, Q
IPR012677Nucleotide-binding alpha-beta plait domain superfamilyHomologous Superfamily
M, N, O, P, Q
IPR035979RNA-binding domain superfamilyHomologous Superfamily
M, N, O, P, Q
IPR034769Cleavage and polyadenylation specificity factor subunit 6, RNA recognition motifDomain