SMTL ID : 3kk1.1

HIV-1 reverse transcriptase-DNA complex with nuceotide inhibitor GS-9148-diphosphate bound in nucleotide site

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.70 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: 4 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:G.436, A:N.460 Water bridges: A:N.460, B:T.302 Salt bridges: A:R.461 SO4.2: 2 residues within 4Å: Chain A: Q.330, Q.340 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.340, A:Q.340 SO4.6: 5 residues within 4Å: Chain C: G.15, G.16, C.17 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: 914.5 3 PLIP interactions: 3 interactions with chain A Metal complexes: 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:D.443, A:E.478, A:D.498, A:D.498

1 x 914: [(2R,5R)-5-(6-aminopurin-9-yl)-4-fluoro-2,5-dihydrofuran-2-yl]oxymethyl-[hydroxy(phosphonooxy)phosphoryl]oxy-phosphinic acid(Non-covalent)

914.5: 17 residues within 4Å: Chain A: K.65, K.70, R.72, L.74, D.110, V.111, G.112, D.113, A.114, Y.115, Q.151, D.185, K.219 Chain C: C.21 Chain D: T.5, G.6 Ligands: MG.3 15 PLIP interactions: 15 interactions with chain A Hydrogen bonds: A:R.72, A:R.72, A:D.113, A:A.114, A:K.219 Water bridges: A:Y.115 Salt bridges: A:K.65, A:K.65, A:K.70, A:R.72, A:R.72, A:K.219 pi-Stacking: A:Y.115 pi-Cation interactions: A:R.72, A:R.72

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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