PDBsum entry 3avc

Recombination/inhibitor

PDB id: 3avc

Contents

Protein chains

149 a.a.

Ligands

SER-ASP-LYS-ILE-ASP-ASN-LEU-ASP ×2

SO4 ×8

ACY ×2

Metals

_CL ×2

Waters ×132

PDB id:

3avc

Name:

Recombination/inhibitor

Title:

Crystal structures of novel allosteric peptide inhibitors of HIV integrase in the ledgf binding site

Structure:

Integrase. Chain: a, b. Fragment: ccd domain (unp residues 1197-1359). Synonym: in. Engineered: yes. Mutation: yes. Ledgf peptide. Chain: d, f. Synonym: lens epithelial derived growth factor.

Source:

Human immunodeficiency virus type 1. HIV-1. Organism_taxid: 11698. Strain: new york-5 isolate. Gene: gag-pol. Expressed in: escherichia coli. Expression_system_taxid: 562. Synthetic: yes. Homo sapiens.

Resolution:

1.77Å R-factor: 0.160 R-free: 0.196

Authors:

T.S.Peat,J.J.Deadman,J.Newman,D.I.Rhodes

Key ref:

D.I.Rhodes et al. (2011). Crystal structures of novel allosteric peptide inhibitors of HIV integrase identify new interactions at the LEDGF binding site. Chembiochem, 12, 2311-2315. PubMed id: 21850718

Date:

02-Mar-11 Release date: 18-Jan-12

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: 149 a.a.*

* PDB and UniProt seqs differ at 2 residue positions (black crosses)

Enzyme reactions

• Enzyme class 1: E.C.2.7.7.- - ?????
• Enzyme class 2: 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: 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: E.C.3.1.-.-
• Enzyme class 5: 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: E.C.3.1.26.13 - retroviral ribonuclease H.
• Enzyme class 7: 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

reference

Chembiochem 12:2311-2315 (2011)

PubMed id: 21850718

Crystal structures of novel allosteric peptide inhibitors of HIV integrase identify new interactions at the LEDGF binding site.

D.I.Rhodes, T.S.Peat, N.Vandegraaff, D.Jeevarajah, J.Newman, J.Martyn, J.A.Coates, N.J.Ede, P.Rea, J.J.Deadman.

ABSTRACT

No abstract given.