PDBsum entry 8fnh

Viral protein/DNA/inhibitor

PDB id: 8fnh

Contents

Protein chains

261 a.a.

242 a.a.

66 a.a.

47 a.a.

DNA/RNA

Ligands

DLU ×2

Metals

_MG ×4

_ZN ×2

Waters ×624

PDB id:

8fnh

Name:

Viral protein/DNA/inhibitor

Title:

Structure of q148k HIV-1 intasome with dolutegravir bound

Structure:

Lamina-associated polypeptide 2, isoform alpha,integrase chimera. Chain: a, b, c, d, g, h, i, j. Synonym: thymopoietin isoform alpha,tp alpha,thymopoietin-related peptide isoform alpha,tprp isoform alpha,in. Engineered: yes. Mutation: yes. DNA (27-mer). Chain: e, k.

Source:

Homo sapiens, human immunodeficiency virus 1. Organism_taxid: 9606, 11676. Gene: tmpo, lap2, gag-pol. Expressed in: escherichia coli. Expression_system_taxid: 562. Synthetic: yes. Human immunodeficiency virus 1. Organism_taxid: 11676. Organism_taxid: 11676

Authors:

Z.L.Shan,D.O.Passos,T.S.Strutzenberg,M.Li,D.Lyumkis

Key ref:

M.Li et al. (2023). Mechanisms of HIV-1 integrase resistance to dolutegra potent inhibition of drug-Resistant variants.. Sci adv, 9, g5953. PubMed id: 37478179

Date:

27-Dec-22 Release date: 09-Aug-23

Protein chains

P12497  (POL_HV1N5) -  Gag-Pol polyprotein from Human immunodeficiency virus type 1 group M subtype B (isolate NY5)

Seq: 1435 a.a.

Struc: 261 a.a.*

Protein chains

P42166  (LAP2A_HUMAN) -  Lamina-associated polypeptide 2, isoform alpha from Homo sapiens

Seq: 694 a.a.

Struc: 261 a.a.*

Protein chains

P12497  (POL_HV1N5) -  Gag-Pol polyprotein from Human immunodeficiency virus type 1 group M subtype B (isolate NY5)

Seq: 1435 a.a.

Struc: 242 a.a.

Protein chains

P42166  (LAP2A_HUMAN) -  Lamina-associated polypeptide 2, isoform alpha from Homo sapiens

Seq: 694 a.a.

Struc: 242 a.a.*

Protein chains

P12497  (POL_HV1N5) -  Gag-Pol polyprotein from Human immunodeficiency virus type 1 group M subtype B (isolate NY5)

Seq: 1435 a.a.

Struc: 66 a.a.

Protein chains

P42166  (LAP2A_HUMAN) -  Lamina-associated polypeptide 2, isoform alpha from Homo sapiens

Seq: 694 a.a.

Struc: 66 a.a.*

Protein chains

P12497  (POL_HV1N5) -  Gag-Pol polyprotein from Human immunodeficiency virus type 1 group M subtype B (isolate NY5)

Seq: 1435 a.a.

Struc: 47 a.a.

Protein chains

P42166  (LAP2A_HUMAN) -  Lamina-associated polypeptide 2, isoform alpha from Homo sapiens

Seq: 694 a.a.

Struc: 47 a.a.*

* PDB and UniProt seqs differ at 529 residue positions (black crosses)

DNA/RNA chains

A-C-T-G-C-T-A-G-A-G-A-T-T-T-T-C-C-C-G 19 bases

C-G-G-G-A-A-A-A-T-C-T-C-T-A-G-C-A 17 bases

A-C-T-G-C-T-A-G-A-G-A-T-T-T-T-C-C-C-G 19 bases

C-G-G-G-A-A-A-A-T-C-T-C-T-A-G-C-A 17 bases

Enzyme reactions

• Enzyme class 2: Chains A, B, C, D, G, H, I, J: E.C.2.7.7.- - ?????
• Enzyme class 3: Chains A, B, C, D, G, H, I, J: E.C.2.7.7.49 - RNA-directed Dna polymerase.
• Reaction: DNA(n) + a 2'-deoxyribonucleoside 5'-triphosphate = DNA(n+1) + diphosphate
• Enzyme class 4: Chains A, B, C, D, G, H, I, J: E.C.2.7.7.7 - DNA-directed Dna polymerase.
• Reaction: DNA(n) + a 2'-deoxyribonucleoside 5'-triphosphate = DNA(n+1) + diphosphate
• Enzyme class 5: Chains A, B, C, D, G, H, I, J: E.C.3.1.-.-
• Enzyme class 6: Chains A, B, C, D, G, H, I, J: E.C.3.1.13.2 - exoribonuclease H.
• Reaction: Exonucleolytic cleavage to 5'-phosphomonoester oligonucleotides in both 5'- to 3'- and 3'- to 5'-directions.
• Enzyme class 7: Chains A, B, C, D, G, H, I, J: E.C.3.1.26.13 - retroviral ribonuclease H.
• Enzyme class 8: Chains A, B, C, D, G, H, I, J: E.C.3.4.23.16 - HIV-1 retropepsin.
• Reaction: Specific for a P1 residue that is hydrophobic, and P1' variable, but often Pro.

Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.

Molecule diagrams generated from .mol files obtained from the KEGG ftp site