Brand  (β version)

PDB ID: 1R0A

Hetero Atom Contents

  The number of atoms exceeds 100,000.
  So, it can not be displayed here.

Select unit:

Select hetatm:   

close
information
centroid:
interaction residue:

Select chain:   Sequence  

Data format:   

Color scheme of protein:

Ligands
Code Name Style Show Link
GOL Glycerol PoSSuM
MG Magnesium ion PoSSuM
GLC Alpha-D-glucopyranose PoSSuM
Non-standard Residues
Code Name Show
2DA 2',3'-dideoxyadenosine-5'-monophosphate
Glycosylation
Code Name Emphasize
Modification
Code Name Show

Structure summary

Code : 1R0A   PDBj   RCSB PDB   PDBe
Header : Transferase/immune system/DNA
Title : Crystal structure of HIV-1 reverse transcriptase covalently tethered to DNA template-primer solved to 2.8 angstroms
Release Data : 2004-08-03
Compound :
mol_id molecule chains
1 5'-D(*A*TP*GP*CP*AP*TP*CP*GP*GP*CP*GP*CP*TP*CP*GP*AP*AP*CP*AP*GP*GP*GP*AP*CP*GP*GP*T)-3' T
other_details: oligonucleotide DNA template
mol_id molecule chains
2 5'-D(*C*CP*GP*TP*CP*CP*CP*TP*GP*TP*TP*CP*GP*AP*GP*CP*GP*CP*CP*GP*(2DA))-3' P
other_details: oligonucleotide DNA primer
mol_id molecule chains
3 Reverse transcriptase A
ec: 2.7.7.49
fragment: HIV-1 RT
other_details: p66
mol_id molecule chains
4 Reverse transcriptase B
ec: 2.7.7.49
fragment: HIV-1 RT
other_details: p51
mol_id molecule chains
5 monoclonal antibody (light chain) L
fragment: fab 28
mol_id molecule chains
6 monoclonal antibody (heavy chain) H
fragment: fab 28
Source :
mol_id organism_scientific
1
synthetic: yes
mol_id organism_scientific
2
synthetic: yes
mol_id organism_scientific expression_system
3 Human immunodeficiency virus 1  (taxid:11676) Escherichia coli  (taxid:562)
gene: POL
mol_id organism_scientific expression_system
4 Human immunodeficiency virus 1  (taxid:11676) Escherichia coli  (taxid:562)
gene: POL
mol_id organism_scientific organism_common
5 Mus musculus  (taxid:10090) House mouse
mol_id organism_scientific organism_common
6 Mus musculus  (taxid:10090) House mouse
Authors : Tuske, S., Ding, J., Arnold, E.
Keywords : HIV-1, Transferase, immune system, DNA, Transferase-immune system-DNA COMPLEX
Exp. method : X-RAY DIFFRACTION ( 2.80 Å )
Citation :

Nonnucleoside inhibitor binding affects the interactions of the fingers subdomain of human immunodeficiency virus type 1 reverse transcriptase with DNA.

Peletskaya, E.N.,Kogon, A.A.,Tuske, S.  et al.
(2004)  J.Virol.  78 : 3387 - 3397

PubMed: 15016861
DOI: 10.1128/JVI.78.7.3387-3397.2004

Reaction

Chain : 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
-
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]
DNA(n) + a 2'-deoxyribonucleoside 5'-triphosphate = DNA(n+1) + diphosphate 		2.7.7.49 PROSITE-ProRule:PRU00405, PubMed:2476069
-
[Reverse transcriptase/ribonuclease H]
DNA(n) + a 2'-deoxyribonucleoside 5'-triphosphate = DNA(n+1) + diphosphate 		2.7.7.7 PROSITE-ProRule:PRU00405, PubMed:2476069
-
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.