Brand  (β version)

PDB ID: 1T05

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Ligands
Code Name Style Show Link
GOL Glycerol PoSSuM
MG Magnesium ion PoSSuM
TNV [2-(6-amino-9h-purin-9-yl)-1-methylethoxy]methyl-triphosphate PoSSuM
Non-standard Residues
Code Name Show
DDG 2',3'-dideoxy-guanosine-5'-monophosphate
MRG N2-(3-mercaptopropyl)-2'-deoxyguanosine-5'-monophosphate
Glycosylation
Code Name Emphasize
Modification
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Structure summary

Code : 1T05   PDBj   RCSB PDB   PDBe
Header : Transferase/DNA
Title : HIV-1 reverse transcriptase crosslinked to template-primer with tenofovir-diphosphate bound as the incoming nucleotide substrate
Release Data : 2004-05-11
Compound :
mol_id molecule chains
1 oligonucleotide template T
mol_id molecule chains
2 oligonucleotide primer P
mol_id molecule chains
3 POL polyprotein A
ec: 2.7.7.49
fragment: HIV-1 reverse transcriptase p66 subunit
mutation: Q258C, C280S
mol_id molecule chains
4 POL polyprotein B
ec: 2.7.7.49
fragment: HIV-1 reverse transcriptase p51 subunit
mutation: C280S
Source :
mol_id organism_scientific
1
synthetic: yes
mol_id organism_scientific
2
synthetic: yes
other_details: chemically modified with thiol-dGMP and enzymatically terminated with ddGTP
mol_id organism_scientific expression_system
3 Human immunodeficiency virus 1  (taxid:11676) Escherichia coli  (taxid:562)
strain: BH10
gene: POL
expression_system_strain: DH5alpha
mol_id organism_scientific expression_system
4 Human immunodeficiency virus 1  (taxid:11676) Escherichia coli  (taxid:562)
strain: BH10
gene: POL
expression_system_strain: DH5alpha
Authors : Tuske, S., Sarafianos, S.G., Ding, J., Arnold, E.
Keywords : HIV-1 reverse transcriptase, tenofovir, RT-DNA complex, Transferase-DNA COMPLEX
Exp. method : X-RAY DIFFRACTION ( 3.0 Å )
Citation :

Structures of HIV-1 RT-DNA complexes before and after incorporation of the anti-AIDS drug tenofovir

Tuske, S.,Sarafianos, S.G.,Clark Jr., A.D.  et al.
(2004)  Nat.Struct.Mol.Biol.  11 : 469 - 474

PubMed: 15107837
DOI: 10.1038/nsmb760

Reaction

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