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HIV-1 reverse transcriptase in complex with DNA that has incorporated EFdA-MP at the P-(post-translocation) site and dTMP at the N-(pre-translocation) site

X-ray diffraction
2.896Å resolution
PDB entry 5j2n coloured by chain, front view.
PDB entry 5j2n coloured by chain, side view.
PDB entry 5j2n coloured by chain, top view.
Source organism: HIV-1 M:B_HXB2R
Assembly composition:
hetero tetramer (preferred)
Entry contents: 2 distinct polypeptide molecules
2 distinct DNA molecules

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Assemblies

Assembly 1 (preferred)
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Assembly Name: Protease and DNA
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Multimeric state: hetero tetramer
Accessible surface area: 47450.97 Å2
Buried surface area: 13947.85 Å2
Dissociation area: 3,111.68 Å2
Dissociation energy (ΔGdiss): 27.95 kcal/mol
Dissociation entropy (TΔSdiss): 15.21 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-118853

Macromolecules

Reverse transcriptase/ribonuclease H
Chain: A
Length: 560 amino acids
Theoretical weight: 64.52 KDa
Source organism: HIV-1 M:B_HXB2R
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P04585 (Residues: 588-1147; Coverage: 39%)
Gene name: gag-pol
Pfam:
InterPro:
CATH:
Reverse transcriptase/ribonuclease H in PDB entry 5j2n, assembly 1, front view.
Reverse transcriptase/ribonuclease H in PDB entry 5j2n, assembly 1, side view.
Reverse transcriptase/ribonuclease H in PDB entry 5j2n, assembly 1, top view.
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p51 RT
Chain: B
Length: 440 amino acids
Theoretical weight: 51.38 KDa
Source organism: HIV-1 M:B_HXB2R
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P04585 (Residues: 588-1027; Coverage: 31%)
Gene name: gag-pol
Pfam:
InterPro:
CATH:
p51 RT in PDB entry 5j2n, assembly 1, front view.
p51 RT in PDB entry 5j2n, assembly 1, side view.
p51 RT in PDB entry 5j2n, assembly 1, top view.
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DNA chain P
Name: DNA 5'-D(*AP*CP*AP*GP*TP*CP*CP*CP*TP*GP*TP*TP*CP*GP*GP*(MRG)P*CP*GP*CP*CP*G)-3'
Representative chains: P
Length: 22 nucleotides
Theoretical weight: 6.82 KDa
DNA 5'-D(*AP*CP*AP*GP*TP*CP*CP*CP*TP*GP*TP*TP*CP*GP*GP*(MRG)P*CP*GP*CP*CP*G)-3' in PDB entry 5j2n, assembly 1, front view.
DNA 5'-D(*AP*CP*AP*GP*TP*CP*CP*CP*TP*GP*TP*TP*CP*GP*GP*(MRG)P*CP*GP*CP*CP*G)-3' in PDB entry 5j2n, assembly 1, side view.
DNA 5'-D(*AP*CP*AP*GP*TP*CP*CP*CP*TP*GP*TP*TP*CP*GP*GP*(MRG)P*CP*GP*CP*CP*G)-3' in PDB entry 5j2n, assembly 1, top view.
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DNA chain T
Name: DNA (27-MER)
Representative chains: T
Length: 27 nucleotides
Theoretical weight: 8.41 KDa
DNA (27-MER) in PDB entry 5j2n, assembly 1, front view.
DNA (27-MER) in PDB entry 5j2n, assembly 1, side view.
DNA (27-MER) in PDB entry 5j2n, assembly 1, top view.
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