Brand  (β version)

PDB ID: 4K4Q

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Ligands
Code Name Style Show Link
06B 3-bromo-2,6-dimethoxybenzoic acid PoSSuM
3TL Benzyl [(1s,4s,7s,8r,9r,10s,13s,16s)-7,10-dibenzyl-8,9-dihydroxy-1,16-dimethyl-4,13-bis(1-methylethyl)-2,5,12,15,18-pentaoxo-20-phenyl-19-oxa-3,6,11,14,17-pentaazaicos-1-yl]carbamate PoSSuM
BME Beta-mercaptoethanol PoSSuM
DMS Dimethyl sulfoxide PoSSuM
NO3 Nitrate ion PoSSuM
Non-standard Residues
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Structure summary

Code : 4K4Q   PDBj   RCSB PDB   PDBe
Header : HYDROLASE/HYDROLASE INHIBITOR
Title : TL-3 inhibited Trp6Ala HIV Protease with 3-bromo-2,6-dimethoxybenzoic acid bound in flap site
Release Data : 2013-09-18
Compound :
mol_id molecule chains
1 HIV-1 protease A,B
ec: 3.4.23.16
mutation: W6A
Source :
mol_id organism_scientific organism_common expression_system
1 Human immunodeficiency virus 1  (taxid:11683) HIV-1 Escherichia coli  (taxid:562)
gene: gag-pol
expression_system_strain: Rosetta2(DE3) pLysS
expression_system_vector_type: plasmid
expression_system_plasmid: pET-21a(+)
Authors : Tiefenbrunn, T., Stout, C.D.
Keywords : fragment binding, exosite, HYDROLASE-HYDROLASE INHIBITOR complex
Exp. method : X-RAY DIFFRACTION ( 1.8000 Å )
Citation :

Crystallographic Fragment-Based Drug Discovery: Use of a Brominated Fragment Library Targeting HIV Protease.

Tiefenbrunn, T.,Forli, S.,Happer, M.  et al.
(2014)  Chem.Biol.Drug Des.  83 : 141 - 148

PubMed: 23998903
DOI: 10.1111/cbdd.12227

Reaction

Chain : A, B
UniProt : P12499 (POL_HV1Z2)
Reaction: EC: Evidence:
Physiological Direction:
Specific for a P1 residue that is hydrophobic, and P1' variable, but often Pro. 3.4.23.16 PROSITE-ProRule:PRU00275
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Endohydrolysis of RNA in RNA/DNA hybrids. Three different cleavage modes: 1. sequence-specific internal cleavage of RNA. Human immunodeficiency virus type 1 and Moloney murine leukemia virus enzymes prefer to cleave the RNA strand one nucleotide away from the RNA-DNA junction. 2. RNA 5'-end directed cleavage 13-19 nucleotides from the RNA end. 3. DNA 3'-end directed cleavage 15-20 nucleotides away from the primer terminus. 3.1.26.13 ECO:0000250
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3'-end directed exonucleolytic cleavage of viral RNA-DNA hybrid. 3.1.13.2 ECO:0000250
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DNA(n) + a 2'-deoxyribonucleoside 5'-triphosphate = DNA(n+1) + diphosphate 2.7.7.49 PROSITE-ProRule:PRU00405
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DNA(n) + a 2'-deoxyribonucleoside 5'-triphosphate = DNA(n+1) + diphosphate 2.7.7.7 PROSITE-ProRule:PRU00405
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Cofactor: Evidence: Note:
Mg(2+) ECO:0000250
Binds 2 magnesium ions for reverse transcriptase polymerase activity.
Mg(2+) ECO:0000250
Binds 2 magnesium ions for ribonuclease H (RNase H) activity. Substrate-binding is a precondition for magnesium binding.
Mg(2+) ECO:0000250
Magnesium ions are required for integrase activity. Binds at least 1, maybe 2 magnesium ions.