SMTL ID : 4dg1.1

Crystal structure of HIV-1 reverse transcriptase (RT) with polymorphism mutation K172A and K173A

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.15 Å

Oligo State

hetero-1-1-mer

Ligands

4 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 7 residues within 4Å: Chain A: Q.269, I.270, Y.339, K.350, T.351, G.352 Ligands: GOL.7 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:T.351, H2O.5 MG.2: 4 residues within 4Å: Chain A: D.443, G.444, E.478, D.498 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.443 MG.3: 3 residues within 4Å: Chain A: P.226, E.233, H.235 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.233, A:H.235, H2O.5 MG.16: 6 residues within 4Å: Chain B: Q.23, N.57, T.58, P.59, F.130, T.131 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:T.58

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

EDO.4: 6 residues within 4Å: Chain A: V.442, V.496, D.498, V.536, I.542, G.543 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:V.496, A:D.498, A:D.498 Water bridges: A:K.540 EDO.5: 3 residues within 4Å: Chain A: E.44, K.46, S.117 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.44, A:K.46 EDO.9: 4 residues within 4Å: Chain A: T.7, D.121, E.122, D.123 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.7, A:E.122, A:D.123, A:D.123 EDO.10: 3 residues within 4Å: Chain A: K.385, T.386 Chain B: T.27 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.386, A:T.386, A:T.386 EDO.12: 3 residues within 4Å: Chain A: L.193, Q.197, K.201 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.197 EDO.13: 9 residues within 4Å: Chain A: L.100, K.101, K.102, K.103, V.106, Y.188, H.235, P.236, Y.318 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.101, A:K.103 Water bridges: A:K.101 EDO.14: 6 residues within 4Å: Chain A: E.370, Q.373, K.374, T.377 Chain B: E.396, T.400 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.373, A:T.377, A:T.377 EDO.15: 6 residues within 4Å: Chain A: T.377, I.380 Chain B: W.24, P.25, T.400 Ligands: EDO.19 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.377 EDO.17: 5 residues within 4Å: Chain A: W.406 Chain B: Q.330, K.331, P.392, V.423 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.331 EDO.18: 3 residues within 4Å: Chain B: P.157, Y.183, M.184 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:M.184 EDO.19: 5 residues within 4Å: Chain B: W.24, E.399, W.402, T.403 Ligands: EDO.15 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:W.24, B:E.399 EDO.20: 6 residues within 4Å: Chain B: R.358, K.366, E.370, E.404, Y.405, Q.407 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.358, B:E.370 EDO.22: 1 residues within 4Å: Chain B: Y.318 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Y.318, B:Y.318 EDO.24: 5 residues within 4Å: Chain B: G.45, P.119, R.125, N.147, V.148 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:G.45, B:R.125, B:N.147 Water bridges: B:R.125

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 5 residues within 4Å: Chain A: K.103, P.176, D.177, I.178, V.179 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.177 GOL.7: 10 residues within 4Å: Chain A: H.96, W.239, Q.269, I.270, V.314, H.315, L.349, K.350, T.351 Ligands: MG.1 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:H.96, A:H.315, A:T.351, A:T.351 GOL.8: 6 residues within 4Å: Chain A: Y.532, A.534, W.535 Chain B: N.255, Q.258, K.259 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:N.255, B:N.255, A:W.535 GOL.11: 3 residues within 4Å: Chain A: K.395, E.396, E.399 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.396, A:E.396, A:E.399 Water bridges: A:E.399 GOL.21: 7 residues within 4Å: Chain B: K.30, I.63, K.64, W.71, T.403, E.404, W.406 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:K.30, B:K.30, B:K.64, B:W.406 GOL.23: 5 residues within 4Å: Chain A: E.6, T.7, K.166 Chain B: G.51, E.53 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:G.51, B:E.53, A:T.7

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hachiya, A. et al., HIV-1 Reverse Transcriptase (RT) Polymorphism 172K Suppresses the Effect of Clinically Relevant Drug Resistance Mutations to Both Nucleoside and Non-nucleoside RT Inhibitors. J.Biol.Chem. (2012)

Release Date

2012-06-20

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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