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Crystal structure of the HIV-1 capsid protein C-terminal domain in complex with a camelid VHH and the CAI peptide. External Resource: Annotation Domain Annotation: SCOP2 Classification SCOP2 Database Homepage Chains Type Family Name Domain Identifier Family Identifier Provenance Source (Version) A SCOP2B Superfamily Retrovirus capsid dimerization domain-like 8037182 3001819 SCOP2B (2022-06-29)
Chains Family Name Domain Identifier Architecture Possible Homology Homology Topology Family Provenance Source (Version) A PF19317 e2xxmA1 A: alpha bundles X: Retrovirus capsid protein H: Retrovirus capsid protein-C (From Topology) T: Retrovirus capsid protein-C F: PF19317 ECOD (1.6) B PF07686 e2xxmB1 A: beta sandwiches X: Immunoglobulin-like beta-sandwich H: Immunoglobulin-related T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like F: PF07686 ECOD (1.6)
Chain Protein Name Description Organism Name Gene Allele Name(s) Domain Name(s) Receptor Type Receptor Description Provenance Source CAMELID VHH 9 VH Vicugna pacos (alpaca) IGHV3S4*01, IGHJ4*01 V-DOMAIN VH IG (VH) IMGT (202416-0)
Chain Chain Class Chain Subclass Chain Type Antigen Name(s) Provenance Source Heavy Chain IGHV1 - capsid protein p24 SAbDab (2024-04-26)
Chains Accession Name Description Comments Source 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
Chains Polymer Molecular Function Biological Process Cellular Component CAPSID PROTEIN P24 catalytic activity, acting on RNA RNA exonuclease activity, producing 5'-phosphomonoesters catalytic activity, acting on a nucleic acid RNA exonuclease activity RNA nuclease activity hydrolase activity exonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 5'-phosphomonoesters nuclease activity hydrolase activity, acting on ester bonds exoribonuclease H activity exonuclease activity catalytic activity catalytic activity, acting on DNA DNA-directed DNA polymerase activity DNA polymerase activity transferase activity nucleotidyltransferase activity transferase activity, transferring phosphorus-containing groups DNA binding binding organic cyclic compound binding nucleic acid binding RNA-directed DNA polymerase activity RNA binding aspartic-type peptidase activity peptidase activity catalytic activity, acting on a protein aspartic-type endopeptidase activity endopeptidase activity lipid binding endonuclease activity RNA endonuclease activity, producing 5'-phosphomonoesters RNA-DNA hybrid ribonuclease activity RNA endonuclease activity endonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 5'-phosphomonoesters structural molecule activity cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding Less CAMELID VHH 9 - - - C [auth T] INHIBITOR OF CAPSID ASSEMBLY - - -
Chains Accession Name Type IPR036397 Ribonuclease H superfamily Homologous Superfamily IPR043128 Reverse transcriptase/Diguanylate cyclase domain Homologous Superfamily IPR001995 Peptidase A2A, retrovirus, catalytic Domain IPR001878 Zinc finger, CCHC-type Domain IPR008919 Retrovirus capsid, N-terminal Homologous Superfamily IPR012344 Matrix protein, lentiviral and alpha-retroviral, N-terminal Homologous Superfamily IPR036862 Integrase, C-terminal domain superfamily, retroviral Homologous Superfamily IPR018061 Retropepsins Domain IPR010661 Reverse transcriptase thumb Domain IPR002156 Ribonuclease H domain Domain IPR036875 Zinc finger, CCHC-type superfamily Homologous Superfamily IPR003308 Integrase, N-terminal zinc-binding domain Domain IPR001584 Integrase, catalytic core Domain IPR045345 Retroviral nucleocapsid Gag protein p24, C-terminal domain Domain IPR010999 Retroviral matrix protein Homologous Superfamily IPR021109 Aspartic peptidase domain superfamily Homologous Superfamily IPR001969 Aspartic peptidase, active site Active Site IPR012337 Ribonuclease H-like superfamily Homologous Superfamily IPR017856 Integrase-like, N-terminal Homologous Superfamily IPR000071 Immunodeficiency lentiviral matrix, N-terminal Domain IPR043502 DNA/RNA polymerase superfamily Homologous Superfamily IPR001037 Integrase, C-terminal, retroviral Domain IPR034170 Retropepsin-like catalytic domain Domain IPR000477 Reverse transcriptase domain Domain IPR010659 Reverse transcriptase connection Domain IPR008916 Retrovirus capsid, C-terminal Homologous Superfamily