Brand  (β version)

PDB ID: 3KK1

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Ligands
Code Name Style Show Link
914 [(2r,5r)-5-(6-aminopurin-9-yl)-4-fluoro-2,5-dihydrofuran-2-yl]oxymethyl-[hydroxy(phosphonooxy)phosphoryl]oxy-phosphinic acid PoSSuM
MG Magnesium ion PoSSuM
SO4 Sulfate ion PoSSuM
Non-standard Residues
Code Name Show
DOC 2',3'-dideoxycytidine-5'-monophosphate
Glycosylation
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Modification
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Structure summary

Code : 3KK1   PDBj   RCSB PDB   PDBe
Header : TRANSFERASE/DNA
Title : HIV-1 reverse transcriptase-DNA complex with nuceotide inhibitor GS-9148-diphosphate bound in nucleotide site
Release Data : 2010-03-23
Compound :
mol_id molecule chains synonym
1 Reverse transcriptase p66 subunit A p66 RT
ec: 2.7.7.49
mutation: C280S, Q258C
mol_id molecule chains synonym
2 Reverse transcriptase p51 subunit B p51 RT
ec: 2.7.7.49
mutation: C280S
mol_id molecule chains
3 5'-D(*AP*CP*A*GP*TP*CP*CP*CP*TP*GP*TP*TP*CP*GP*GP*GP*CP*GP*CP*CP*(DOC))-3' P
other_details: primer DNA
mol_id molecule chains
4 5'-D(*A*TP*GP*GP*TP*GP*GP*GP*CP*GP*CP*CP*CP*GP*AP*AP*CP*AP*GP*GP*GP*AP*CP*TP*GP*TP*G)-3' T
other_details: template DNA
Source :
mol_id organism_scientific organism_common expression_system
1 Human immunodeficiency virus type 1  (taxid:11706) HIV-1 Escherichia coli  (taxid:469008)
strain: HXB2D
gene: gag-pol
expression_system_strain: BL21(DE3)
expression_system_vector_type: plasmid
expression_system_plasmid: pET14b
mol_id organism_scientific organism_common expression_system
2 Human immunodeficiency virus type 1  (taxid:11706) HIV-1 Escherichia coli  (taxid:469008)
strain: HXB2D
gene: gag-pol
expression_system_strain: BL21(DE3)
expression_system_vector_type: plasmid
expression_system_plasmid: pET14b
mol_id organism_scientific
3
synthetic: yes
mol_id organism_scientific
4
synthetic: yes
Authors : Lansdon, E.B.
Keywords : HIV, reverse transcriptase, protein-DNA complex, TRANSFERASE-DNA complex
Exp. method : X-RAY DIFFRACTION ( 2.70 Å )
Citation :

Visualizing the molecular interactions of a nucleotide analog, GS-9148, with HIV-1 reverse transcriptase-DNA complex.

Lansdon, E.B.,Samuel, D.,Lagpacan, L.  et al.
(2010)  J.Mol.Biol.  397 : 967 - 978

PubMed: 20156454
DOI: 10.1016/j.jmb.2010.02.019

Reaction

Chain : B
UniProt : P04585 (POL_HV1H2)
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, PubMed:32053707, PubMed:33542150
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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 UniProtKB:P03366
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3'-end directed exonucleolytic cleavage of viral RNA-DNA hybrid. 3.1.13.2 -
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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.