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

ChainsDomain InfoClassFoldSuperfamilyFamilyDomainSpeciesProvenance Source (Version)
Ad3h4ea2 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)
Ad3h4ea1 All alpha proteins Retrovirus capsid protein, N-terminal core domain Retrovirus capsid protein, N-terminal core domain Retrovirus capsid protein, N-terminal core domain automated matches HIV-1 (Human immunodeficiency virus type 1 (NEW YORK-5 ISOLATE) ) [TaxId: 11698 ], SCOPe (2.08)
Bd3h4eb2 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)
Bd3h4eb1 All alpha proteins Retrovirus capsid protein, N-terminal core domain Retrovirus capsid protein, N-terminal core domain Retrovirus capsid protein, N-terminal core domain automated matches HIV-1 (Human immunodeficiency virus type 1 (NEW YORK-5 ISOLATE) ) [TaxId: 11698 ], SCOPe (2.08)
Cd3h4ec2 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)
Cd3h4ec1 All alpha proteins Retrovirus capsid protein, N-terminal core domain Retrovirus capsid protein, N-terminal core domain Retrovirus capsid protein, N-terminal core domain automated matches HIV-1 (Human immunodeficiency virus type 1 (NEW YORK-5 ISOLATE) ) [TaxId: 11698 ], SCOPe (2.08)
Dd3h4ed2 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)
Dd3h4ed1 All alpha proteins Retrovirus capsid protein, N-terminal core domain Retrovirus capsid protein, N-terminal core domain Retrovirus capsid protein, N-terminal core domain automated matches HIV-1 (Human immunodeficiency virus type 1 (NEW YORK-5 ISOLATE) ) [TaxId: 11698 ], SCOPe (2.08)
Ed3h4ee2 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)
Ed3h4ee1 All alpha proteins Retrovirus capsid protein, N-terminal core domain Retrovirus capsid protein, N-terminal core domain Retrovirus capsid protein, N-terminal core domain automated matches HIV-1 (Human immunodeficiency virus type 1 (NEW YORK-5 ISOLATE) ) [TaxId: 11698 ], SCOPe (2.08)
Fd3h4ef2 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)
Fd3h4ef1 All alpha proteins Retrovirus capsid protein, N-terminal core domain Retrovirus capsid protein, N-terminal core domain Retrovirus capsid protein, N-terminal core domain automated matches HIV-1 (Human immunodeficiency virus type 1 (NEW YORK-5 ISOLATE) ) [TaxId: 11698 ], SCOPe (2.08)
Gd3h4eg2 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)
Gd3h4eg1 All alpha proteins Retrovirus capsid protein, N-terminal core domain Retrovirus capsid protein, N-terminal core domain Retrovirus capsid protein, N-terminal core domain automated matches HIV-1 (Human immunodeficiency virus type 1 (NEW YORK-5 ISOLATE) ) [TaxId: 11698 ], SCOPe (2.08)
Hd3h4eh2 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)
Hd3h4eh1 All alpha proteins Retrovirus capsid protein, N-terminal core domain Retrovirus capsid protein, N-terminal core domain Retrovirus capsid protein, N-terminal core domain automated matches HIV-1 (Human immunodeficiency virus type 1 (NEW YORK-5 ISOLATE) ) [TaxId: 11698 ], SCOPe (2.08)
Id3h4ei2 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)
Id3h4ei1 All alpha proteins Retrovirus capsid protein, N-terminal core domain Retrovirus capsid protein, N-terminal core domain Retrovirus capsid protein, N-terminal core domain automated matches HIV-1 (Human immunodeficiency virus type 1 (NEW YORK-5 ISOLATE) ) [TaxId: 11698 ], SCOPe (2.08)
Jd3h4ej2 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)
Jd3h4ej1 All alpha proteins Retrovirus capsid protein, N-terminal core domain Retrovirus capsid protein, N-terminal core domain Retrovirus capsid protein, N-terminal core domain automated matches HIV-1 (Human immunodeficiency virus type 1 (NEW YORK-5 ISOLATE) ) [TaxId: 11698 ], SCOPe (2.08)
Kd3h4ek2 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)
Kd3h4ek1 All alpha proteins Retrovirus capsid protein, N-terminal core domain Retrovirus capsid protein, N-terminal core domain Retrovirus capsid protein, N-terminal core domain automated matches HIV-1 (Human immunodeficiency virus type 1 (NEW YORK-5 ISOLATE) ) [TaxId: 11698 ], SCOPe (2.08)
Ld3h4el2 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)
Ld3h4el1 All alpha proteins Retrovirus capsid protein, N-terminal core domain Retrovirus capsid protein, N-terminal core domain Retrovirus capsid protein, N-terminal core domain automated matches 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 8037182 3001819 SCOP2B (2022-06-29)
BSCOP2B SuperfamilyRetrovirus capsid dimerization domain-like 8037182 3001819 SCOP2B (2022-06-29)
CSCOP2B SuperfamilyRetrovirus capsid dimerization domain-like 8037182 3001819 SCOP2B (2022-06-29)
DSCOP2B SuperfamilyRetrovirus capsid dimerization domain-like 8037182 3001819 SCOP2B (2022-06-29)
ESCOP2B SuperfamilyRetrovirus capsid dimerization domain-like 8037182 3001819 SCOP2B (2022-06-29)
FSCOP2B SuperfamilyRetrovirus capsid dimerization domain-like 8037182 3001819 SCOP2B (2022-06-29)
GSCOP2B SuperfamilyRetrovirus capsid dimerization domain-like 8037182 3001819 SCOP2B (2022-06-29)
HSCOP2B SuperfamilyRetrovirus capsid dimerization domain-like 8037182 3001819 SCOP2B (2022-06-29)
ISCOP2B SuperfamilyRetrovirus capsid dimerization domain-like 8037182 3001819 SCOP2B (2022-06-29)
JSCOP2B SuperfamilyRetrovirus capsid dimerization domain-like 8037182 3001819 SCOP2B (2022-06-29)
KSCOP2B SuperfamilyRetrovirus capsid dimerization domain-like 8037182 3001819 SCOP2B (2022-06-29)
LSCOP2B SuperfamilyRetrovirus capsid dimerization domain-like 8037182 3001819 SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

ChainsFamily NameDomain Identifier ArchitecturePossible HomologyHomologyTopologyFamilyProvenance Source (Version)
AGag_p24_Ce3h4eA1 A: alpha bundlesX: Retrovirus capsid proteinH: Retrovirus capsid protein-C (From Topology)T: Retrovirus capsid protein-CF: Gag_p24_CECOD (1.6)
AGag_p24_Ne3h4eA2 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_Ce3h4eB1 A: alpha bundlesX: Retrovirus capsid proteinH: Retrovirus capsid protein-C (From Topology)T: Retrovirus capsid protein-CF: Gag_p24_CECOD (1.6)
BGag_p24_Ne3h4eB2 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_Ce3h4eC1 A: alpha bundlesX: Retrovirus capsid proteinH: Retrovirus capsid protein-C (From Topology)T: Retrovirus capsid protein-CF: Gag_p24_CECOD (1.6)
CGag_p24_Ne3h4eC2 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_Ce3h4eD6 A: alpha bundlesX: Retrovirus capsid proteinH: Retrovirus capsid protein-C (From Topology)T: Retrovirus capsid protein-CF: Gag_p24_CECOD (1.6)
DGag_p24_Ne3h4eD5 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_Ce3h4eE1 A: alpha bundlesX: Retrovirus capsid proteinH: Retrovirus capsid protein-C (From Topology)T: Retrovirus capsid protein-CF: Gag_p24_CECOD (1.6)
EGag_p24_Ne3h4eE2 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_Ce3h4eF1 A: alpha bundlesX: Retrovirus capsid proteinH: Retrovirus capsid protein-C (From Topology)T: Retrovirus capsid protein-CF: Gag_p24_CECOD (1.6)
FGag_p24_Ne3h4eF2 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_Ce3h4eG1 A: alpha bundlesX: Retrovirus capsid proteinH: Retrovirus capsid protein-C (From Topology)T: Retrovirus capsid protein-CF: Gag_p24_CECOD (1.6)
GGag_p24_Ne3h4eG2 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_Ce3h4eH1 A: alpha bundlesX: Retrovirus capsid proteinH: Retrovirus capsid protein-C (From Topology)T: Retrovirus capsid protein-CF: Gag_p24_CECOD (1.6)
HGag_p24_Ne3h4eH2 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_Ce3h4eI1 A: alpha bundlesX: Retrovirus capsid proteinH: Retrovirus capsid protein-C (From Topology)T: Retrovirus capsid protein-CF: Gag_p24_CECOD (1.6)
IGag_p24_Ne3h4eI2 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_Ce3h4eJ1 A: alpha bundlesX: Retrovirus capsid proteinH: Retrovirus capsid protein-C (From Topology)T: Retrovirus capsid protein-CF: Gag_p24_CECOD (1.6)
JGag_p24_Ne3h4eJ2 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_Ce3h4eK4 A: alpha bundlesX: Retrovirus capsid proteinH: Retrovirus capsid protein-C (From Topology)T: Retrovirus capsid protein-CF: Gag_p24_CECOD (1.6)
KGag_p24_Ne3h4eK3 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_Ce3h4eL1 A: alpha bundlesX: Retrovirus capsid proteinH: Retrovirus capsid protein-C (From Topology)T: Retrovirus capsid protein-CF: Gag_p24_CECOD (1.6)
LGag_p24_Ne3h4eL2 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
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

InterPro: Protein Family Classification InterPro Database Homepage

ChainsAccessionNameType
A, B, C, D, E
IPR036397Ribonuclease H superfamilyHomologous Superfamily
A, B, C, D, E
IPR043128Reverse transcriptase/Diguanylate cyclase domainHomologous Superfamily
A, B, C, D, E
IPR001995Peptidase A2A, retrovirus, catalyticDomain
A, B, C, D, E
IPR001878Zinc finger, CCHC-typeDomain
A, B, C, D, E
IPR008919Retrovirus capsid, N-terminalHomologous Superfamily
A, B, C, D, E
IPR012344Matrix protein, lentiviral and alpha-retroviral, N-terminalHomologous Superfamily
A, B, C, D, E
IPR036862Integrase, C-terminal domain superfamily, retroviralHomologous Superfamily
A, B, C, D, E
IPR018061RetropepsinsDomain
A, B, C, D, E
IPR010661Reverse transcriptase thumbDomain
A, B, C, D, E
IPR002156Ribonuclease H domainDomain
A, B, C, D, E
IPR036875Zinc finger, CCHC-type superfamilyHomologous Superfamily
A, B, C, D, E
IPR003308Integrase, N-terminal zinc-binding domainDomain
A, B, C, D, E
IPR001584Integrase, catalytic coreDomain
A, B, C, D, E
IPR045345Retroviral nucleocapsid Gag protein p24, C-terminal domainDomain
A, B, C, D, E
IPR010999Retroviral matrix proteinHomologous Superfamily
A, B, C, D, E
IPR021109Aspartic peptidase domain superfamilyHomologous Superfamily
A, B, C, D, E
IPR001969Aspartic peptidase, active siteActive Site
A, B, C, D, E
IPR012337Ribonuclease H-like superfamilyHomologous Superfamily
A, B, C, D, E
IPR017856Integrase-like, N-terminalHomologous Superfamily
A, B, C, D, E
IPR000071Immunodeficiency lentiviral matrix, N-terminalDomain
A, B, C, D, E
IPR043502DNA/RNA polymerase superfamilyHomologous Superfamily
A, B, C, D, E
IPR001037Integrase, C-terminal, retroviralDomain
A, B, C, D, E
IPR034170Retropepsin-like catalytic domainDomain
A, B, C, D, E
IPR000477Reverse transcriptase domainDomain
A, B, C, D, E
IPR010659Reverse transcriptase connectionDomain
A, B, C, D, E
IPR008916Retrovirus capsid, C-terminalHomologous Superfamily