PDBsum entry 4g1q

Transferase, hydrolase/inhibitor

PDB id: 4g1q

Contents

Protein chains

556 a.a.

416 a.a.

Ligands

T27

SO4 ×6

EDO ×5

Metals

_MG

Waters ×824

PDB id:

4g1q

Name:

Transferase, hydrolase/inhibitor

Title:

Crystal structure of HIV-1 reverse transcriptase (rt) in complex with rilpivirine (tmc278, edurant), a non-nucleoside rt-inhibiting drug

Structure:

Reverse transcriptase/ribonuclease h. Chain: a. Fragment: p66, unp residues 600-1154. Synonym: exoribonuclease h, p66 rt. Engineered: yes. Mutation: yes. P51 rt. Chain: b. Fragment: p51, unp residues 600-1027.

Source:

Human immunodeficiency virus type 1. HIV-1. Organism_taxid: 11678. Strain: bh10 isolate. Gene: gag-pol. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

1.51Å R-factor: 0.155 R-free: 0.193

Authors:

J.D.Bauman,D.Patel,K.Das,E.Arnold

Key ref:

D.G.Kuroda et al. (2013). Snapshot of the equilibrium dynamics of a drug bound to HIV-1 reverse transcriptase. Nat Chem, 5, 174-181. PubMed id: 23422558 DOI: 10.1038/nchem.1559

Date:

11-Jul-12 Release date: 06-Feb-13

Protein chain

P03366  (POL_HV1B1) -  Gag-Pol polyprotein from Human immunodeficiency virus type 1 group M subtype B (isolate BH10)

Seq: 1447 a.a.

Struc: 556 a.a.*

Protein chain

P03366  (POL_HV1B1) -  Gag-Pol polyprotein from Human immunodeficiency virus type 1 group M subtype B (isolate BH10)

Seq: 1447 a.a.

Struc: 416 a.a.*

* PDB and UniProt seqs differ at 6 residue positions (black crosses)

Enzyme reactions

• Enzyme class 1: Chains A, B: E.C.2.7.7.- - ?????
• Enzyme class 2: Chains A, B: 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: Chains A, B: 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: Chains A, B: E.C.3.1.-.-
• Enzyme class 5: Chains A, B: 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: Chains A, B: E.C.3.1.26.13 - retroviral ribonuclease H.
• Enzyme class 7: Chains A, B: 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: 10.1038/nchem.1559

Nat Chem 5:174-181 (2013)

PubMed id: 23422558

Snapshot of the equilibrium dynamics of a drug bound to HIV-1 reverse transcriptase.

D.G.Kuroda, J.D.Bauman, J.R.Challa, D.Patel, T.Troxler, K.Das, E.Arnold, R.M.Hochstrasser.

ABSTRACT

No abstract given.