PDBsum entry 4obj

Hydrolase

PDB id: 4obj

Contents

Protein chains

99 a.a.

Ligands

ARG-PRO-GLY-ASN-PHE-LEU-GLN-ASN-ARG-PRO

GOL ×3

ACT ×3

EDO ×6

Waters ×160

PDB id:

4obj

Name:

Hydrolase

Title:

Crystal structure of inactive HIV-1 protease in complex with the p1-p6 substrate variant (s451n)

Structure:

HIV-1 protease. Chain: a, b. Synonym: pr, retropepsin. Engineered: yes. Mutation: yes. P1-p6 peptide. Chain: c. Fragment: unp residues 446-455. Engineered: yes.

Source:

Human immunodeficiency virus type 1. HIV-1. Organism_taxid: 11685. Strain: group m subtype b (isolate arv2/sf2). Gene: gag-pol. Expressed in: escherichia coli. Expression_system_taxid: 562. Synthetic: yes. Human immunodeficiency virus 1.

Resolution:

1.75Å R-factor: 0.145 R-free: 0.183

Authors:

M.Kolli

Key ref:

M.Kolli et al. (2014). HIV-1 protease-substrate coevolution in nelfinavir resistance. J Virol, 88, 7145-7154. PubMed id: 24719428 DOI: 10.1128/JVI.00266-14

Date:

07-Jan-14 Release date: 26-Nov-14

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
• 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: 10.1128/JVI.00266-14

J Virol 88:7145-7154 (2014)

PubMed id: 24719428

HIV-1 protease-substrate coevolution in nelfinavir resistance.

M.Kolli, A.Ozen, N.Kurt-Yilmaz, C.A.Schiffer.

ABSTRACT

No abstract given.