PDBsum entry 4y1c

Transferase/transferase binding protein

PDB id: 4y1c

Contents

Protein chains

145 a.a.

Ligands

LYS-DIL-ASP-ASN-45F-PRO

SO4 ×2

Metals

_CD ×4

Waters ×24

PDB id:

4y1c

Name:

Transferase/transferase binding protein

Title:

Cyclic hexapeptide cyc[ndpoppkid] in complex with HIV-1 integrase core domain

Structure:

Integrase. Chain: a, b. Fragment: residues 50-212. Engineered: yes. Mutation: yes. Cyclic hexapeptide cyc[ndpoppkid]. Chain: c. Engineered: yes

Source:

Human immunodeficiency virus 1. Organism_taxid: 11676. Expressed in: escherichia coli k-12. Expression_system_taxid: 83333. Synthetic: yes. Synthetic construct. Organism_taxid: 32630

Resolution:

2.30Å R-factor: 0.246 R-free: 0.295

Authors:

J.Wielens,D.K.Chalmers

Key ref:

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

Date:

07-Feb-15 Release date: 25-Feb-15

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: 145 a.a.*

* PDB and UniProt seqs differ at 4 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