PDBsum entry 4cf0

Transferase

PDB id: 4cf0

Contents

Protein chains

149 a.a.

Ligands

SO4 ×6

O5U ×2

ACT ×2

Waters ×107

PDB id:

4cf0

Name:

Transferase

Title:

Interrogating HIV integrase for compounds that bind- a sampl challenge

Structure:

Integrase. Chain: a, b. Fragment: catalytic domain, residues 50-212. Engineered: yes. Mutation: yes

Source:

Human immunodeficiency virus 1. Organism_taxid: 11676. Strain: type1. Expressed in: escherichia coli. Expression_system_taxid: 511693.

Resolution:

1.85Å R-factor: 0.198 R-free: 0.225

Authors:

T.S.Peat

Key ref:

T.S.Peat et al. (2014). Interrogating HIV integrase for compounds that bind--a SAMPL challenge. J Comput Aided Mol Des, 28, 347-362. PubMed id: 24532034 DOI: 10.1007/s10822-014-9721-7

Date:

13-Nov-13 Release date: 20-Nov-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: 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

DOI no: 10.1007/s10822-014-9721-7

J Comput Aided Mol Des 28:347-362 (2014)

PubMed id: 24532034

Interrogating HIV integrase for compounds that bind--a SAMPL challenge.

T.S.Peat, O.Dolezal, J.Newman, D.Mobley, J.J.Deadman.

ABSTRACT

Tremendous gains and novel methods are often developed when people are challenged to do something new or difficult. This process is enhanced when people compete against each other-this can be seen in sport as well as in science and technology (e.g. the space race). The SAMPL challenges, like the CASP challenges, aim to challenge modellers and software developers to develop new ways of looking at molecular interactions so the community as a whole can progress in the accurate prediction of these interactions. In order for this challenge to occur, data must be supplied so the prospective test can be done. We have supplied unpublished data related to a drug discovery program run several years ago on HIV integrase for the SAMPL4 challenge. This paper describes the methods used to obtain these data and the chemistry involved.