SMTL ID : 6p3v.1

Crystal structure of Eis from Mycobacterium tuberculosis in complex with inhibitor SGT416

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-hexamer

Ligands

6 x NRV: N,N-diethyl-2-[(8-fluoro-5-methyl-5H-[1,2,4]triazino[5,6-b]indol-3-yl)sulfanyl]ethan-1-amine(Non-covalent)

NRV.1: 14 residues within 4Å: Chain A: W.33, D.46, F.47, A.53, W.56, R.57, V.60, L.83, M.85, S.103, F.104, E.421, F.422 Ligands: DMS.3 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:D.46, A:W.56, A:W.56, A:V.60, A:L.83, A:E.421 Salt bridges: A:D.46, A:E.421 pi-Stacking: A:W.56, A:W.56, A:F.104 NRV.4: 14 residues within 4Å: Chain B: W.33, D.46, F.47, A.53, W.56, R.57, V.60, L.83, M.85, S.103, F.104, E.421, F.422 Ligands: DMS.6 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:D.46, B:W.56, B:W.56, B:V.60, B:L.83, B:E.421 Salt bridges: B:D.46, B:E.421 pi-Stacking: B:W.56, B:W.56, B:F.104 NRV.7: 14 residues within 4Å: Chain C: W.33, D.46, F.47, A.53, W.56, R.57, V.60, L.83, M.85, S.103, F.104, E.421, F.422 Ligands: DMS.9 11 PLIP interactions: 11 interactions with chain C Hydrophobic interactions: C:D.46, C:W.56, C:W.56, C:V.60, C:L.83, C:E.421 Salt bridges: C:D.46, C:E.421 pi-Stacking: C:W.56, C:W.56, C:F.104 NRV.10: 14 residues within 4Å: Chain D: W.33, D.46, F.47, A.53, W.56, R.57, V.60, L.83, M.85, S.103, F.104, E.421, F.422 Ligands: DMS.12 11 PLIP interactions: 11 interactions with chain D Hydrophobic interactions: D:D.46, D:W.56, D:W.56, D:V.60, D:L.83, D:E.421 Salt bridges: D:D.46, D:E.421 pi-Stacking: D:W.56, D:W.56, D:F.104 NRV.13: 14 residues within 4Å: Chain E: W.33, D.46, F.47, A.53, W.56, R.57, V.60, L.83, M.85, S.103, F.104, E.421, F.422 Ligands: DMS.15 11 PLIP interactions: 11 interactions with chain E Hydrophobic interactions: E:D.46, E:W.56, E:W.56, E:V.60, E:L.83, E:E.421 Salt bridges: E:D.46, E:E.421 pi-Stacking: E:W.56, E:W.56, E:F.104 NRV.16: 14 residues within 4Å: Chain F: W.33, D.46, F.47, A.53, W.56, R.57, V.60, L.83, M.85, S.103, F.104, E.421, F.422 Ligands: DMS.18 11 PLIP interactions: 11 interactions with chain F Hydrophobic interactions: F:D.46, F:W.56, F:W.56, F:V.60, F:L.83, F:E.421 Salt bridges: F:D.46, F:E.421 pi-Stacking: F:W.56, F:W.56, F:F.104

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

SO4.2: 6 residues within 4Å: Chain A: R.262, I.288, T.289, H.290, Q.417, T.418 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:T.289, A:T.418, A:T.418 Water bridges: A:L.261, A:T.289 Salt bridges: A:R.262 SO4.5: 6 residues within 4Å: Chain B: R.262, I.288, T.289, H.290, Q.417, T.418 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:T.289, B:T.418, B:T.418 Water bridges: B:L.261, B:T.289 Salt bridges: B:R.262 SO4.8: 6 residues within 4Å: Chain C: R.262, I.288, T.289, H.290, Q.417, T.418 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:T.289, C:T.418, C:T.418 Water bridges: C:L.261, C:T.289 Salt bridges: C:R.262 SO4.11: 6 residues within 4Å: Chain D: R.262, I.288, T.289, H.290, Q.417, T.418 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:T.418, D:T.418 Water bridges: D:L.261, D:T.289, D:T.418 Salt bridges: D:R.262 SO4.14: 6 residues within 4Å: Chain E: R.262, I.288, T.289, H.290, Q.417, T.418 6 PLIP interactions: 6 interactions with chain E Hydrogen bonds: E:T.418, E:T.418 Water bridges: E:L.261, E:T.289, E:T.418 Salt bridges: E:R.262 SO4.17: 6 residues within 4Å: Chain F: R.262, I.288, T.289, H.290, Q.417, T.418 6 PLIP interactions: 6 interactions with chain F Hydrogen bonds: F:T.418, F:T.418 Water bridges: F:L.261, F:T.289, F:T.418 Salt bridges: F:R.262

6 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.3: 5 residues within 4Å: Chain A: F.44, D.46, S.103, F.104 Ligands: NRV.1 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:F.104 Water bridges: A:V.105 Salt bridges: A:D.46 pi-Cation interactions: A:F.44 DMS.6: 5 residues within 4Å: Chain B: F.44, D.46, S.103, F.104 Ligands: NRV.4 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:F.104 Water bridges: B:V.105 Salt bridges: B:D.46 pi-Cation interactions: B:F.44 DMS.9: 5 residues within 4Å: Chain C: F.44, D.46, S.103, F.104 Ligands: NRV.7 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:F.104 Water bridges: C:V.105 Salt bridges: C:D.46 pi-Cation interactions: C:F.44 DMS.12: 5 residues within 4Å: Chain D: F.44, D.46, S.103, F.104 Ligands: NRV.10 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:F.104 Water bridges: D:V.105 Salt bridges: D:D.46 pi-Cation interactions: D:F.44 DMS.15: 5 residues within 4Å: Chain E: F.44, D.46, S.103, F.104 Ligands: NRV.13 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:F.104 Water bridges: E:V.105 Salt bridges: E:D.46 pi-Cation interactions: E:F.44 DMS.18: 5 residues within 4Å: Chain F: F.44, D.46, S.103, F.104 Ligands: NRV.16 4 PLIP interactions: 4 interactions with chain F Hydrogen bonds: F:F.104 Water bridges: F:V.105 Salt bridges: F:D.46 pi-Cation interactions: F:F.44

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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