PDBsum entry 6wpf

Transferase/DNA

PDB id: 6wpf

Contents

Protein chains

555 a.a.

394 a.a.

DNA/RNA

Ligands

D4M

SO4 ×4

D4T

GOL

Metals

_MG ×3

Waters ×139

PDB id:

6wpf

Name:

Transferase/DNA

Title:

Structure of HIV-1 reverse transcriptase (rt) in complex with dsdna and d4t

Structure:

DNA primer 21-mer. Chain: p. Engineered: yes. DNA template 27-mer. Chain: t. Engineered: yes. Reverse transcriptase/ribonuclease h. Chain: a. Synonym: pr160gag-pol.

Source:

Synthetic: yes. Synthetic construct. Organism_taxid: 32630. Human immunodeficiency virus type 1 group m subtype b (isolate hxb2). HIV-1. Organism_taxid: 11706. Strain: isolate hxb2. Gene: gag-pol.

Resolution:

2.53Å R-factor: 0.184 R-free: 0.231

Authors:

N.Bertoletti,K.S.Anderson

Key ref:

N.Bertoletti et al. (2020). Post-Catalytic complexes with emtricitabine or stavud HIV-1 reverse transcriptase reveal new mechanistic in for nucleotide incorporation and drug resistance.. Molecules, 25, . PubMed id: 33096918

Date:

27-Apr-20 Release date: 04-Nov-20

Protein chain

P04585  (POL_HV1H2) -  Gag-Pol polyprotein from Human immunodeficiency virus type 1 group M subtype B (isolate HXB2)

Seq: 1435 a.a.

Struc: 555 a.a.*

Protein chain

P04585  (POL_HV1H2) -  Gag-Pol polyprotein from Human immunodeficiency virus type 1 group M subtype B (isolate HXB2)

Seq: 1435 a.a.

Struc: 394 a.a.*

* PDB and UniProt seqs differ at 3 residue positions (black crosses)

DNA/RNA chains

G-T-C-C-C-T-G-T-T-C-G-G-G47-C-G-C-C-G 18 bases

G-G-A-C-G-G-C-G-C-C-C-G-A-A-C-A-G-G-G-A-C-T-G 23 bases

Enzyme reactions

• Enzyme class 1: Chains A, B: E.C.2.7.7.- - ?????
• Enzyme class 2: Chains A, B: E.C.2.7.7.49 - RNA-directed Dna polymerase.
• Reaction: DNA(n) + a 2'-deoxyribonucleoside 5'-triphosphate = DNA(n+1) + diphosphate
• Enzyme class 3: Chains A, B: E.C.2.7.7.7 - DNA-directed Dna polymerase.
• Reaction: DNA(n) + a 2'-deoxyribonucleoside 5'-triphosphate = DNA(n+1) + diphosphate
• Enzyme class 4: Chains A, B: E.C.3.1.-.-
• Enzyme class 5: Chains A, B: 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 6: Chains A, B: E.C.3.1.26.13 - retroviral ribonuclease H.
• Enzyme class 7: Chains A, B: 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