SMTL ID : 4pqu.1 (1 other biounit)

Crystal structure of HIV-1 Reverse Transcriptase in complex with RNA/DNA and dATP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.51 Å

Oligo State

hetero-1-1-mer

Ligands

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

DTP.1: 18 residues within 4Å: Chain A: K.67, R.74, L.76, D.112, V.113, G.114, D.115, A.116, Y.117, Q.153, M.186, D.187, K.221 Chain C: U.5, C.6 Chain D: G.21 Ligands: MG.2, MG.3 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:Y.117 Hydrogen bonds: A:D.115, A:D.115, A:A.116, A:Y.117, A:Q.153 Salt bridges: A:K.67, A:K.67, A:R.74, A:R.74, A:K.221 pi-Cation interactions: A:R.74

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 5 residues within 4Å: Chain A: D.112, V.113, D.187 Ligands: DTP.1, MG.3 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.112, A:V.113, A:D.187 MG.3: 6 residues within 4Å: Chain A: D.112, D.187, D.188 Chain D: G.21 Ligands: DTP.1, MG.2 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.112, A:D.187, A:D.187, A:D.188, H2O.4

1 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.4: 6 residues within 4Å: Chain A: K.368, Q.409, A.410, T.411 Chain B: Q.394, T.397 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:Q.394, A:A.410, A:T.411 Water bridges: A:K.368

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

SO4.5: 9 residues within 4Å: Chain A: L.102, K.103, K.104, K.105, V.108, Y.190, H.237, P.238, Y.320 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.103, A:K.105, A:Y.320 Salt bridges: A:K.104 SO4.6: 3 residues within 4Å: Chain A: K.333, G.335, Q.336 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.336 Salt bridges: A:K.333 SO4.7: 6 residues within 4Å: Chain A: W.428, Y.429, Q.430, L.527, K.530, E.531 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.430, A:L.527, A:E.531 Water bridges: A:V.533 SO4.8: 4 residues within 4Å: Chain B: W.24, E.399, W.402, T.403 1 PLIP interactions: 1 interactions with chain B Water bridges: B:W.402 SO4.10: 5 residues within 4Å: Chain B: W.266, P.420, P.421, L.422, V.423 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:L.422, B:V.423, B:V.423

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.9: 6 residues within 4Å: Chain A: T.379, I.382 Chain B: P.25, T.400, T.403, E.404 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:T.403, B:T.403, A:T.379 Water bridges: B:K.30, B:K.30

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Das, K. et al., Structures of HIV-1 RT-RNA/DNA ternary complexes with dATP and nevirapine reveal conformational flexibility of RNA/DNA: insights into requirements for RNase H cleavage. Nucleic Acids Res. (2014)

Release Date

2014-06-18

Peptides

HIV-1 Reverse Transcriptase, p66 subunit: A
HIV-1 Reverse Transcriptase, p51 subunit: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

HIV-1 Reverse Transcriptase, p66 subunit

HIV-1 Reverse Transcriptase, p51 subunit

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