PDBsum entry 3oy4

Hydrolase/hydrolase inhibitor

PDB id: 3oy4

Contents

Protein chains

99 a.a. *

Ligands

PO4 ×4

ACT ×7

017

Waters ×144

* Residue conservation analysis

PDB id:

3oy4

Name:

Hydrolase/hydrolase inhibitor

Title:

Crystal structure of HIV-1 l76v protease in complex with the protease inhibitor darunavir.

Structure:

HIV-1 protease. Chain: a, b. Synonym: retropepsin, pr. Engineered: yes. Mutation: yes

Source:

Human immunodeficiency virus type 1. HIV-1. Organism_taxid: 11685. Strain: sf2. Gene: gag-pol. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

1.76Å R-factor: 0.180 R-free: 0.219

Authors:

C.A.Schiffer,E.A.Nalivaika,R.M.Bandaranayake

Key ref:

C.A.Schiffer et al. Crystal structure of HIV-1 l76V protease in complex w protease inhibitor darunavir.. To be published, .

Date:

22-Sep-10 Release date: 09-Feb-11

Protein chains

P03369  (POL_HV1A2) -  Gag-Pol polyprotein from Human immunodeficiency virus type 1 group M subtype B (isolate ARV2/SF2)

Seq: 1437 a.a.

Struc: 99 a.a.*

* PDB and UniProt seqs differ at 3 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

DNA(n) + 2'-deoxyribonucleoside 5'-triphosphate = DNA(n+1) (Bound ligand (Het Group name = PO4) matches with 55.56% similarity) + 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

DNA(n) + 2'-deoxyribonucleoside 5'-triphosphate = DNA(n+1) (Bound ligand (Het Group name = PO4) matches with 55.56% similarity) + 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