PDBsum entry 3s3m

Recombination/inhibitor/DNA

PDB id: 3s3m

Contents

Protein chains

368 a.a.

184 a.a.

DNA/RNA

Ligands

SO4 ×2

GOL ×4

NH4

DLU

HEZ

Metals

_ZN

_MG ×2

Waters ×235

PDB id:

3s3m

Name:

Recombination/inhibitor/DNA

Title:

Crystal structure of the prototype foamy virus (pfv) intasome in complex with magnesium and dolutegravir (s/gsk1349572)

Structure:

Pfv integrase. Chain: a, b. Synonym: in, p42in. Engineered: yes. 5'-d( Ap Tp Tp Gp Tp Cp Ap Tp Gp Gp Ap Ap Tp Tp Tp Cp Gp Cp A)-3'. Chain: c. Engineered: yes. Other_details: 19 nucleotide preprocessed pfv donor DNA (non-

Source:

Human spumaretrovirus. Sfvcpz(hu), human foamy virus. Organism_taxid: 11963. Strain: hsrv2. Gene: pol. Expressed in: escherichia coli. Expression_system_taxid: 562. Synthetic: yes. Other_details: synthesized oligonucleotide.

Resolution:

2.49Å R-factor: 0.207 R-free: 0.232

Authors:

S.Hare,P.Cherepanov

Key ref:

S.Hare et al. (2011). Structural and functional analyses of the second-generation integrase strand transfer inhibitor dolutegravir (S/GSK1349572). Mol Pharmacol, 80, 565-572. PubMed id: 21719464

Date:

18-May-11 Release date: 13-Jul-11

Protein chain

P14350  (POL_FOAMV) -  Pro-Pol polyprotein from Human spumaretrovirus

Seq: 1143 a.a.

Struc: 368 a.a.*

Protein chain

P14350  (POL_FOAMV) -  Pro-Pol polyprotein from Human spumaretrovirus

Seq: 1143 a.a.

Struc: 184 a.a.*

* PDB and UniProt seqs differ at 4 residue positions (black crosses)

DNA/RNA chains

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

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

Enzyme reactions

• Enzyme class 2: Chains A, B: E.C.2.7.7.- - ?????
• Enzyme class 3: 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 4: 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 5: Chains A, B: E.C.3.1.-.-
• Enzyme class 6: Chains A, B: E.C.3.1.26.4 - ribonuclease H.
• Reaction: Endonucleolytic cleavage to 5'-phosphomonoester.
• Enzyme class 7: Chains A, B: E.C.3.4.23.- - ?????

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

reference

Mol Pharmacol 80:565-572 (2011)

PubMed id: 21719464

Structural and functional analyses of the second-generation integrase strand transfer inhibitor dolutegravir (S/GSK1349572).

S.Hare, S.J.Smith, M.Métifiot, A.Jaxa-Chamiec, Y.Pommier, S.H.Hughes, P.Cherepanov.

ABSTRACT

No abstract given.