Brand  (β version)

PDB ID: 4DMN

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Ligands
Code Name Style Show Link
ARS Arsenic PoSSuM
SO4 Sulfate ion PoSSuM
0L9 (2s)-[6-bromo-4-(4-chlorophenyl)-2-methylquinolin-3-yl](methoxy)ethanoic acid PoSSuM
Non-standard Residues
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Structure summary

Code : 4DMN   PDBj   RCSB PDB   PDBe
Header : VIRAL PROTEIN/Inhibitor
Title : HIV-1 Integrase Catalytical Core Domain
Release Data : 2012-03-21
Compound :
mol_id molecule chains synonym
1 HIV-1 Integrase A IN
Source :
mol_id organism_scientific organism_common expression_system
1 Human immunodeficiency virus type 1  (taxid:11698) HIV-1 Escherichia coli  (taxid:469008)
gene: gag-pol
expression_system_strain: BL21(DE3)
expression_system_vector_type: plasmid
Authors : Feng, L., Kvaratskhelia, M.
Keywords : Integrase, CCD, DDE motif, dimer interface, VIRAL PROTEIN-Inhibitor complex
Exp. method : X-RAY DIFFRACTION ( 2.4500 Å )
Citation :

Multimode, cooperative mechanism of action of allosteric HIV-1 integrase inhibitors.

Kessl, J.J.,Jena, N.,Koh, Y.  et al.
(2012)  J.Biol.Chem.  287 : 16801 - 16811

PubMed: 22437836
DOI: 10.1074/jbc.M112.354373

Reaction

Chain : A
UniProt : P12497 (POL_HV1N5)
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.