PDBsum entry 3nxn

Hydrolase/hydrolase inhibitor

PDB id: 3nxn

Contents

Protein chain

203 a.a.

Ligands

KVS

SO4 ×4

Waters ×98

PDB id:

3nxn

Name:

Hydrolase/hydrolase inhibitor

Title:

X-ray structure of ester chemical analogue 'covalent dimer' [ile50,o- ile50']hiv-1 protease complexed with kvs-1 inhibitor

Structure:

Protease covalent dimer. Chain: a. Engineered: yes

Source:

Synthetic: yes. Other_details: chemical protein synthesis

Resolution:

1.80Å R-factor: 0.195 R-free: 0.225

Authors:

V.Y.Torbeev,S.B.H.Kent

Key ref:

V.Y.Torbeev et al. (2011). Protein conformational dynamics in the mechanism of HIV-1 protease catalysis. Proc Natl Acad Sci U S A, 108, 20982-20987. PubMed id: 22158985

Date:

14-Jul-10 Release date: 02-Nov-11

Protein chain

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

Seq: 1437 a.a.

Struc: 203 a.a.*

* PDB and UniProt seqs differ at 97 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

Proc Natl Acad Sci U S A 108:20982-20987 (2011)

PubMed id: 22158985

Protein conformational dynamics in the mechanism of HIV-1 protease catalysis.

V.Y.Torbeev, H.Raghuraman, D.Hamelberg, M.Tonelli, W.M.Westler, E.Perozo, S.B.Kent.

ABSTRACT

No abstract given.