PDBsum entry 3wnh

Viral protein/peptide

PDB id: 3wnh

Contents

Protein chains

137 a.a.

Ligands

PRO-LYS-NLE-ASP-ASN-DVA ×2

SO4 ×6

Metals

_CD ×4

_CL ×2

Waters ×241

PDB id:

3wnh

Name:

Viral protein/peptide

Title:

Cyclic hexapeptide pkzdnv in complex with HIV-1 integrase

Structure:

Gag-pol polyprotein. Chain: a, b. Fragment: catalytic core domain, unp residue 1203-1359. Synonym: HIV-1 integrase. Engineered: yes. Mutation: yes. Pk(nle)dn(dva) peptide. Chain: c, d. Engineered: yes

Source:

Human immunodeficiency virus type 1. HIV-1. Organism_taxid: 11698. Strain: nl43. Gene: HIV-1 pol. Expressed in: escherichia coli. Expression_system_taxid: 562. Synthetic: yes. Other_details: synthetic peptide

Resolution:

1.50Å R-factor: 0.192 R-free: 0.227

Authors:

J.Wielens,D.K.Chalmers,M.W.Parker

Key ref:

S.E.Northfield et al. Hexapeptide mimetics of ledgf in complex with HIV-1 integrase. To be published, .

Date:

10-Dec-13 Release date: 25-Dec-13

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: 137 a.a.*

* PDB and UniProt seqs differ at 5 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