Brand  (β version)

PDB ID: 3TOG

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Ligands
Code Name Style Show Link
DMS Dimethyl sulfoxide PoSSuM
079 (S)-N-((2s,3s,4r,5r)-4-amino-3,5-dihydroxy-1,6-diphenylhexan-2-yl)-3-methyl-2-(2-phenoxyacetamido)butanamide PoSSuM
Non-standard Residues
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Structure summary

Code : 3TOG   PDBj   RCSB PDB   PDBe
Header : HYDROLASE/HYDROLASE INHIBITOR
Title : HIV-1 Protease - Epoxydic Inhibitor Complex (pH 9 - Monoclinic Crystal form P21)
Release Data : 2012-08-15
Compound :
mol_id molecule chains synonym
1 Gag-Pol polyprotein A,B,C,D Pr160Gag-Pol, Matrix protein p17, MA, Capsid protein p24, CA, Spacer peptide p2, Nucleocapsid protein p7, NC, Transframe peptide, TF, p6-pol, p6*, Protease, PR, Retropepsin, Reverse transcriptase/ribonuclease H, Exoribonuclease H, p66 RT, p51 RT, p15, Integrase, IN
ec: 3.4.23.16, 2.7.7.49, 2.7.7.7, 3.1.26.13, 3.1.13.2
fragment: UNP Residues 501-599
mutation: Q507K L533I L563I C567A C595A
Source :
mol_id organism_scientific organism_common expression_system
1 Human immunodeficiency virus type 1 (BRU ISOLATE)  (taxid:11686) HIV-1 Escherichia coli  (taxid:469008)
gene: gag-pol
expression_system_strain: BL21(DE3)
expression_system_vector_type: plasmid
expression_system_plasmid: pET11A
Authors : Geremia, S., Olajuyigbe, F.M., Demitri, N.
Keywords : HIV PR, epoxide, in-crystal reaction, hydrolase, HYDROLASE-HYDROLASE INHIBITOR complex
Exp. method : X-RAY DIFFRACTION ( 1.24 Å )
Citation :

Developing HIV-1 Protease Inhibitors through Stereospecific Reactions in Protein Crystals.

Olajuyigbe, F.M.,Demitri, N.,De Zorzi, R.  et al.
(2016)  Molecules  21

PubMed: 27809253
DOI: 10.3390/molecules21111458

Reaction

Chain : A, B, C, D
UniProt : P03367 (POL_HV1BR)
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 -
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3'-end directed exonucleolytic cleavage of viral RNA-DNA hybrid. 3.1.13.2 -
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a 2'-deoxyribonucleoside 5'-triphosphate + DNA(n) = diphosphate + DNA(n+1) 2.7.7.49 PROSITE- ProRule:PRU00405
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a 2'-deoxyribonucleoside 5'-triphosphate + DNA(n) = diphosphate + DNA(n+1) 2.7.7.7 PROSITE- ProRule:PRU00405
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