SMTL ID : 3kk2.1

HIV-1 reverse transcriptase-DNA complex with dATP bound in the nucleotide binding site

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.90 Å

Oligo State

hetero-1-1-mer

Ligands

3 x SO4: SULFATE ION(Non-functional Binders)

SO4.1: 5 residues within 4Å: Chain A: G.436, A.437, N.460, R.461 Chain B: A.300 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:G.436, A:A.437, A:N.460, A:N.460 Salt bridges: A:R.461 SO4.2: 2 residues within 4Å: Chain A: E.328, Q.340 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.340 Water bridges: A:E.328, A:E.328 SO4.6: 5 residues within 4Å: Chain C: G.14, G.15, G.16 Chain D: G.10, C.11 No protein-ligand interaction detected (PLIP)

2 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 4 residues within 4Å: Chain A: D.110, V.111, D.185 Ligands: DTP.5 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.110, A:D.110, A:V.111, A:D.185 MG.4: 4 residues within 4Å: Chain A: D.443, G.444, E.478, D.498 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.443, A:E.478, A:E.478, A:D.498, A:D.498

1 x DTP: 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE(Non-covalent)

DTP.5: 17 residues within 4Å: Chain A: K.65, K.70, R.72, D.110, V.111, G.112, D.113, A.114, Y.115, Q.151, M.184, D.185, K.219 Chain C: C.21 Chain D: T.5, G.6 Ligands: MG.3 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:Y.115, A:Q.151 Hydrogen bonds: A:D.113, A:A.114, A:Y.115 Water bridges: A:K.65, A:K.65, A:K.70, A:K.70 Salt bridges: A:K.65, A:K.65, A:K.70, A:R.72, A:R.72, A:K.219, A:K.219

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lansdon, E.B. et al., Visualizing the molecular interactions of a nucleotide analog, GS-9148, with HIV-1 reverse transcriptase-DNA complex. J.Mol.Biol. (2010)

Release Date

2010-03-23

Peptides

Reverse transcriptase p66 subunit: A
Reverse transcriptase p51 subunit: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Reverse transcriptase p66 subunit

Reverse transcriptase p51 subunit

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