SMTL ID : 6p3u.1

Crystal structure of Eis from Mycobacterium tuberculosis in complex with inhibitor SGT335

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.55 Å

Oligo State

homo-hexamer

Ligands

6 x NRY: 1-(4-fluorophenyl)-2-[2-(4-fluorophenyl)-2-oxoethyl]pyrrolo[1,2-a]pyrazin-2-ium(Non-covalent)

NRY.1: 16 residues within 4Å: Chain A: W.33, D.46, F.47, I.48, S.52, A.53, W.56, R.57, V.60, L.83, M.85, S.103, F.104, E.421, F.422 Ligands: SO4.9 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:I.48, A:I.48, A:W.56, A:V.60, A:L.83 Hydrogen bonds: A:S.103 pi-Stacking: A:W.56, A:F.104 NRY.10: 16 residues within 4Å: Chain B: W.33, D.46, F.47, I.48, S.52, A.53, W.56, R.57, V.60, L.83, M.85, S.103, F.104, E.421, F.422 Ligands: SO4.18 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:I.48, B:I.48, B:W.56, B:V.60, B:L.83 Hydrogen bonds: B:S.103 pi-Stacking: B:W.56, B:F.104 NRY.19: 16 residues within 4Å: Chain C: W.33, D.46, F.47, I.48, S.52, A.53, W.56, R.57, V.60, L.83, M.85, S.103, F.104, E.421, F.422 Ligands: SO4.27 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: C:I.48, C:I.48, C:W.56, C:V.60, C:L.83 Hydrogen bonds: C:S.103 pi-Stacking: C:W.56, C:F.104 NRY.28: 16 residues within 4Å: Chain D: W.33, D.46, F.47, I.48, S.52, A.53, W.56, R.57, V.60, L.83, M.85, S.103, F.104, E.421, F.422 Ligands: SO4.36 9 PLIP interactions: 9 interactions with chain D Hydrophobic interactions: D:I.48, D:I.48, D:W.56, D:V.60, D:L.83 Hydrogen bonds: D:S.103, D:F.422 pi-Stacking: D:W.56, D:F.104 NRY.37: 16 residues within 4Å: Chain E: W.33, D.46, F.47, I.48, S.52, A.53, W.56, R.57, V.60, L.83, M.85, S.103, F.104, E.421, F.422 Ligands: SO4.45 9 PLIP interactions: 9 interactions with chain E Hydrophobic interactions: E:I.48, E:I.48, E:W.56, E:V.60, E:L.83 Hydrogen bonds: E:S.103, E:F.422 pi-Stacking: E:W.56, E:F.104 NRY.46: 16 residues within 4Å: Chain F: W.33, D.46, F.47, I.48, S.52, A.53, W.56, R.57, V.60, L.83, M.85, S.103, F.104, E.421, F.422 Ligands: SO4.54 9 PLIP interactions: 9 interactions with chain F Hydrophobic interactions: F:I.48, F:I.48, F:W.56, F:V.60, F:L.83 Hydrogen bonds: F:S.103, F:F.422 pi-Stacking: F:W.56, F:F.104

12 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 4 residues within 4Å: Chain A: H.125, R.317, M.319, R.373 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:H.125, A:R.317, A:R.317, A:M.319, A:R.373 Water bridges: A:R.126 GOL.3: 5 residues within 4Å: Chain A: P.61, T.62, Y.84, S.131, Y.133 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.62, A:Y.84, A:S.131, A:Y.133, A:Y.133 GOL.11: 4 residues within 4Å: Chain B: H.125, R.317, M.319, R.373 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:H.125, B:R.317, B:R.317, B:M.319, B:R.373 Water bridges: B:R.126 GOL.12: 5 residues within 4Å: Chain B: P.61, T.62, Y.84, S.131, Y.133 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:T.62, B:Y.84, B:S.131, B:Y.133, B:Y.133 GOL.20: 4 residues within 4Å: Chain C: H.125, R.317, M.319, R.373 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:H.125, C:R.317, C:R.317, C:M.319, C:R.373 Water bridges: C:R.126 GOL.21: 5 residues within 4Å: Chain C: P.61, T.62, Y.84, S.131, Y.133 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:T.62, C:Y.84, C:S.131, C:Y.133, C:Y.133 GOL.29: 4 residues within 4Å: Chain D: H.125, R.317, M.319, R.373 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:H.125, D:R.317, D:R.317, D:M.319, D:R.373 Water bridges: D:R.126 GOL.30: 5 residues within 4Å: Chain D: P.61, T.62, Y.84, S.131, Y.133 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:T.62, D:Y.84, D:S.131, D:Y.133 GOL.38: 4 residues within 4Å: Chain E: H.125, R.317, M.319, R.373 6 PLIP interactions: 6 interactions with chain E Hydrogen bonds: E:H.125, E:R.317, E:R.317, E:M.319, E:R.373 Water bridges: E:R.126 GOL.39: 5 residues within 4Å: Chain E: P.61, T.62, Y.84, S.131, Y.133 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:T.62, E:Y.84, E:S.131, E:Y.133 GOL.47: 4 residues within 4Å: Chain F: H.125, R.317, M.319, R.373 6 PLIP interactions: 6 interactions with chain F Hydrogen bonds: F:H.125, F:R.317, F:R.317, F:M.319, F:R.373 Water bridges: F:R.126 GOL.48: 5 residues within 4Å: Chain F: P.61, T.62, Y.84, S.131, Y.133 4 PLIP interactions: 4 interactions with chain F Hydrogen bonds: F:T.62, F:Y.84, F:S.131, F:Y.133

6 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.4: 10 residues within 4Å: Chain A: L.261, R.262, H.269, I.287, I.288, T.289, H.290, D.293, Q.417 Ligands: SO4.7 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:L.261, A:R.262, A:H.269, A:T.289 PEG.13: 10 residues within 4Å: Chain B: L.261, R.262, H.269, I.287, I.288, T.289, H.290, D.293, Q.417 Ligands: SO4.16 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:L.261, B:R.262, B:H.269, B:T.289 PEG.22: 10 residues within 4Å: Chain C: L.261, R.262, H.269, I.287, I.288, T.289, H.290, D.293, Q.417 Ligands: SO4.25 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:L.261, C:R.262, C:H.269, C:T.289 PEG.31: 10 residues within 4Å: Chain D: L.261, R.262, H.269, I.287, I.288, T.289, H.290, D.293, Q.417 Ligands: SO4.34 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:L.261, D:R.262, D:H.269 PEG.40: 10 residues within 4Å: Chain E: L.261, R.262, H.269, I.287, I.288, T.289, H.290, D.293, Q.417 Ligands: SO4.43 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:L.261, E:R.262, E:H.269 PEG.49: 10 residues within 4Å: Chain F: L.261, R.262, H.269, I.287, I.288, T.289, H.290, D.293, Q.417 Ligands: SO4.52 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:L.261, F:R.262, F:H.269

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

SO4.5: 8 residues within 4Å: Chain A: P.92, G.93, R.328, G.329, Y.330, A.331, S.412, D.413 Ligand excluded by PLIP SO4.6: 6 residues within 4Å: Chain A: W.33, R.57, V.60, P.61, T.62, A.65 Ligand excluded by PLIP SO4.7: 7 residues within 4Å: Chain A: R.262, I.288, T.289, H.290, Q.417, T.418 Ligands: PEG.4 Ligand excluded by PLIP SO4.8: 7 residues within 4Å: Chain A: A.367, E.368, I.369, E.370, R.396, T.397, K.398 Ligand excluded by PLIP SO4.9: 6 residues within 4Å: Chain A: F.44, D.46, S.103, F.104, F.422 Ligands: NRY.1 Ligand excluded by PLIP SO4.14: 8 residues within 4Å: Chain B: P.92, G.93, R.328, G.329, Y.330, A.331, S.412, D.413 Ligand excluded by PLIP SO4.15: 6 residues within 4Å: Chain B: W.33, R.57, V.60, P.61, T.62, A.65 Ligand excluded by PLIP SO4.16: 7 residues within 4Å: Chain B: R.262, I.288, T.289, H.290, Q.417, T.418 Ligands: PEG.13 Ligand excluded by PLIP SO4.17: 7 residues within 4Å: Chain B: A.367, E.368, I.369, E.370, R.396, T.397, K.398 Ligand excluded by PLIP SO4.18: 6 residues within 4Å: Chain B: F.44, D.46, S.103, F.104, F.422 Ligands: NRY.10 Ligand excluded by PLIP SO4.23: 8 residues within 4Å: Chain C: P.92, G.93, R.328, G.329, Y.330, A.331, S.412, D.413 Ligand excluded by PLIP SO4.24: 6 residues within 4Å: Chain C: W.33, R.57, V.60, P.61, T.62, A.65 Ligand excluded by PLIP SO4.25: 7 residues within 4Å: Chain C: R.262, I.288, T.289, H.290, Q.417, T.418 Ligands: PEG.22 Ligand excluded by PLIP SO4.26: 7 residues within 4Å: Chain C: A.367, E.368, I.369, E.370, R.396, T.397, K.398 Ligand excluded by PLIP SO4.27: 6 residues within 4Å: Chain C: F.44, D.46, S.103, F.104, F.422 Ligands: NRY.19 Ligand excluded by PLIP SO4.32: 8 residues within 4Å: Chain D: P.92, G.93, R.328, G.329, Y.330, A.331, S.412, D.413 Ligand excluded by PLIP SO4.33: 6 residues within 4Å: Chain D: W.33, R.57, V.60, P.61, T.62, A.65 Ligand excluded by PLIP SO4.34: 7 residues within 4Å: Chain D: R.262, I.288, T.289, H.290, Q.417, T.418 Ligands: PEG.31 Ligand excluded by PLIP SO4.35: 7 residues within 4Å: Chain D: A.367, E.368, I.369, E.370, R.396, T.397, K.398 Ligand excluded by PLIP SO4.36: 6 residues within 4Å: Chain D: F.44, D.46, S.103, F.104, F.422 Ligands: NRY.28 Ligand excluded by PLIP SO4.41: 8 residues within 4Å: Chain E: P.92, G.93, R.328, G.329, Y.330, A.331, S.412, D.413 Ligand excluded by PLIP SO4.42: 6 residues within 4Å: Chain E: W.33, R.57, V.60, P.61, T.62, A.65 Ligand excluded by PLIP SO4.43: 7 residues within 4Å: Chain E: R.262, I.288, T.289, H.290, Q.417, T.418 Ligands: PEG.40 Ligand excluded by PLIP SO4.44: 7 residues within 4Å: Chain E: A.367, E.368, I.369, E.370, R.396, T.397, K.398 Ligand excluded by PLIP SO4.45: 6 residues within 4Å: Chain E: F.44, D.46, S.103, F.104, F.422 Ligands: NRY.37 Ligand excluded by PLIP SO4.50: 8 residues within 4Å: Chain F: P.92, G.93, R.328, G.329, Y.330, A.331, S.412, D.413 Ligand excluded by PLIP SO4.51: 6 residues within 4Å: Chain F: W.33, R.57, V.60, P.61, T.62, A.65 Ligand excluded by PLIP SO4.52: 7 residues within 4Å: Chain F: R.262, I.288, T.289, H.290, Q.417, T.418 Ligands: PEG.49 Ligand excluded by PLIP SO4.53: 7 residues within 4Å: Chain F: A.367, E.368, I.369, E.370, R.396, T.397, K.398 Ligand excluded by PLIP SO4.54: 6 residues within 4Å: Chain F: F.44, D.46, S.103, F.104, F.422 Ligands: NRY.46 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Green, K.D. et al., Probing the Robustness of Inhibitors of Tuberculosis Aminoglycoside Resistance Enzyme Eis by Mutagenesis. Acs Infect Dis. (2019)

Release Date

2019-09-04

Peptides

N-acetyltransferase Eis: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

E
A

F
A

N-acetyltransferase Eis

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