Brand  (β version)

PDB ID: 4QAG

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Ligands
Code Name Style Show Link
MN Manganese (II) ion PoSSuM
F95 (7,8-dihydroxy-2-oxo-2h-chromen-4-yl)acetic acid PoSSuM
Non-standard Residues
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Glycosylation
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Structure summary

Code : 4QAG   PDBj   RCSB PDB   PDBe
Header : HYDROLASE/HYDROLASE INHIBITOR
Title : Structure of a dihydroxycoumarin active-site inhibitor in complex with the RNASE H domain of HIV-1 reverse transcriptase
Release Data : 2014-06-04
Compound :
mol_id molecule chains synonym
1 Reverse transcriptase/ribonuclease H A,B Exoribonuclease H, p66 RT
ec: 2.7.7.49, 2.7.7.7, 3.1.26.13, 3.1.13.2
fragment: UNP residues 1024-1156
Source :
mol_id organism_scientific organism_common expression_system
1 Human immunodeficiency virus type 1  (taxid:11678) HIV-1 ESCHERICHIA COLI  (taxid:469008)
gene: gag-pol
expression_system_strain: BL21(DE3)
expression_system_vector_type: plasmid
expression_system_plasmid: pLysS
Authors : Himmel, D.M., Ho, W.C., Arnold, E.
Keywords : RNASE H INHIBITOR, STRUCTURE-BASED DRUG DESIGN, ACTIVE SITE, TRANSFERASE, DIHYDROXYCOUMARIN ANALOGS, DIHYDROXY-BENZOPYRONE DERIVATIVES, DIVALENT CATION CHELATOR, AIDS, REVERSE TRANSCRIPTASE, PROTEIN-INHIBITOR COMPLEX, HYDROLASE-HYDROLASE INHIBITOR complex
Exp. method : X-RAY DIFFRACTION ( 1.7120 Å )
Citation :

Structure of a Dihydroxycoumarin Active-Site Inhibitor in Complex with the RNase H Domain of HIV-1 Reverse Transcriptase and Structure-Activity Analysis of Inhibitor Analogs.

Himmel, D.M.,Myshakina, N.S.,Ilina, T.  et al.
(2014)  J.Mol.Biol.  426 : 2617 - 2631

PubMed: 24840303
DOI: 10.1016/j.jmb.2014.05.006

Structure of HIV-1 Reverse Transcriptase with the Inhibitor beta-Thujaplicinol Bound at the RNase H Active Site

Himmel, D.M.,Maegley, K.A.,Pauly, T.A.  et al.
(2009)  Structure  17 : 1625 - 1635

Synthesis, Activity, and Structural Analysis of Novel ALPHA-HYDROXYTROPOLONE INHIBITORS OF HUMAN IMMUNODEFICIENCY VIRUS REVERSE TRANSCRIPTASE-ASSOCIATED RIBONUCLEASE H

Chung, S.,Himmel, D.M.,Jiang, J.  et al.
(2011)  J.Med.Chem.  54 : 4462 - 4473

HIGH-RESOLUTION STRUCTURES OF HIV-1 REVERSE TRANSCRIPTASE/TMC278 COMPLEXES: STRATEGIC FLEXIBILITY EXPLAINS POTENCY AGAINST RESISTANCE MUTATIONS

Das, K.,Bauman, J.D.,Clark Jr., A.D.  et al.
(2008)  Proc.Natl.Acad.Sci.USA  105 : 1466 - 1471

HIV-1 REVERSE TRANSCRIPTASE STRUCTURE WITH RNASE H INHIBITOR DIHYDROXY BENZOYL NAPHTHYL HYDRAZONE BOUND AT A NOVEL SITE

Himmel, D.M.,Sarafianos, S.G.,Dharmasena, S.  et al.
(2006)  ACS CHEM.BIOL.  1 : 702 - 712

Reaction

Chain : A, B
UniProt : P03366 (POL_HV1B1)
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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3'-end directed exonucleolytic cleavage of viral RNA-DNA hybrid. 3.1.13.2 ECO:0000250
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[Reverse transcriptase/ribonuclease H]
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 PubMed:2476069
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[Reverse transcriptase/ribonuclease H]
a 2'-deoxyribonucleoside 5'-triphosphate + DNA(n) = diphosphate + DNA(n+1) 		2.7.7.49 PROSITE- ProRule:PRU00405, PubMed:2476069
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[Reverse transcriptase/ribonuclease H]
a 2'-deoxyribonucleoside 5'-triphosphate + DNA(n) = diphosphate + DNA(n+1) 		2.7.7.7 PROSITE- ProRule:PRU00405, PubMed:2476069
-