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Crystal structure of HIV-1 reverse transcriptase (RT) with DNA and the nonnucleoside inhibitor nevirapine

X-ray diffraction
2.85Å resolution
PDB entry 3v81 coloured by chain, front view.
PDB entry 3v81 coloured by chain, side view.
PDB entry 3v81 coloured by chain, top view.
Source organism: Human immunodeficiency virus type 1 BH10
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: 50899.64 Å2
Buried surface area: 12403.53 Å2
Dissociation area: 1,790.74 Å2
Dissociation energy (ΔGdiss): 17.7 kcal/mol
Dissociation entropy (TΔSdiss): 13 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-117031
Assembly 2
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Assembly Name: Protease and DNA
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Multimeric state: hetero tetramer
Accessible surface area: 51297.14 Å2
Buried surface area: 12297.4 Å2
Dissociation area: 1,881.56 Å2
Dissociation energy (ΔGdiss): 14.84 kcal/mol
Dissociation entropy (TΔSdiss): 13.02 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-117031

Macromolecules

Reverse transcriptase/ribonuclease H
Chains: A, C
Length: 556 amino acids
Theoretical weight: 64.02 KDa
Source organism: Human immunodeficiency virus type 1 BH10
Expression system: Escherichia coli
UniProt:
  • Canonical: P03366 (Residues: 600-1153; Coverage: 38%)
Gene name: gag-pol
Pfam:
InterPro:
CATH:
Reverse transcriptase/ribonuclease H in PDB entry 3v81, assembly 1, front view.
Reverse transcriptase/ribonuclease H in PDB entry 3v81, assembly 1, side view.
Reverse transcriptase/ribonuclease H in PDB entry 3v81, assembly 1, top view.
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p51 RT
Chains: B, D
Length: 428 amino acids
Theoretical weight: 50.04 KDa
Source organism: Human immunodeficiency virus type 1 BH10
Expression system: Escherichia coli
UniProt:
  • Canonical: P03366 (Residues: 600-1027; Coverage: 30%)
Gene name: gag-pol
Pfam:
InterPro:
CATH:
p51 RT in PDB entry 3v81, assembly 1, front view.
p51 RT in PDB entry 3v81, assembly 1, side view.
p51 RT in PDB entry 3v81, assembly 1, top view.
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DNA chains E, T
Name: DNA (5'-D(*AP*TP*GP*GP*AP*AP*GP*GP*CP*GP*CP*CP*CP*GP*AP*AP*CP*AP*GP*GP*GP*AP*CP*TP*GP*TP*G)-3')
Representative chains: E, T
Length: 27 nucleotides
Theoretical weight: 8.42 KDa
DNA (5'-D(*AP*TP*GP*GP*AP*AP*GP*GP*CP*GP*CP*CP*CP*GP*AP*AP*CP*AP*GP*GP*GP*AP*CP*TP*GP*TP*G)-3') in PDB entry 3v81, assembly 1, front view.
DNA (5'-D(*AP*TP*GP*GP*AP*AP*GP*GP*CP*GP*CP*CP*CP*GP*AP*AP*CP*AP*GP*GP*GP*AP*CP*TP*GP*TP*G)-3') in PDB entry 3v81, assembly 1, side view.
DNA (5'-D(*AP*TP*GP*GP*AP*AP*GP*GP*CP*GP*CP*CP*CP*GP*AP*AP*CP*AP*GP*GP*GP*AP*CP*TP*GP*TP*G)-3') in PDB entry 3v81, assembly 1, top view.
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DNA chains F, P
Name: DNA (5'-D(*A*CP*AP*GP*TP*CP*CP*CP*TP*GP*TP*TP*CP*GP*GP*(MRG)P*CP*GP*CP*CP*(ATM))-3')
Representative chains: F, P
Length: 21 nucleotides
Theoretical weight: 6.49 KDa
DNA (5'-D(*A*CP*AP*GP*TP*CP*CP*CP*TP*GP*TP*TP*CP*GP*GP*(MRG)P*CP*GP*CP*CP*(ATM))-3') in PDB entry 3v81, assembly 1, front view.
DNA (5'-D(*A*CP*AP*GP*TP*CP*CP*CP*TP*GP*TP*TP*CP*GP*GP*(MRG)P*CP*GP*CP*CP*(ATM))-3') in PDB entry 3v81, assembly 1, side view.
DNA (5'-D(*A*CP*AP*GP*TP*CP*CP*CP*TP*GP*TP*TP*CP*GP*GP*(MRG)P*CP*GP*CP*CP*(ATM))-3') in PDB entry 3v81, assembly 1, top view.
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