SMTL ID : 8f51.1

Crystal structure of acetyltransferase Eis from M. tuberculosis in complex with mefloquine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.35 Å

Oligo State

homo-hexamer

Ligands

6 x YMZ: Mefloquine(Non-covalent)

YMZ.1: 16 residues within 4Å: Chain A: W.33, F.37, F.44, D.46, F.47, G.49, S.52, A.53, W.56, R.57, V.60, L.83, M.85, S.103, F.104, F.422 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:F.44, A:W.56, A:W.56, A:L.83 Hydrogen bonds: A:W.56 Water bridges: A:S.103 Halogen bonds: A:A.53 YMZ.8: 16 residues within 4Å: Chain B: W.33, F.37, F.44, D.46, F.47, G.49, S.52, A.53, W.56, R.57, V.60, L.83, M.85, S.103, F.104, F.422 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:F.44, B:W.56, B:W.56, B:L.83 Hydrogen bonds: B:W.56 Water bridges: B:S.103 Halogen bonds: B:A.53 YMZ.15: 16 residues within 4Å: Chain C: W.33, F.37, F.44, D.46, F.47, G.49, S.52, A.53, W.56, R.57, V.60, L.83, M.85, S.103, F.104, F.422 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:F.44, C:W.56, C:W.56, C:L.83 Hydrogen bonds: C:W.56 Water bridges: C:S.103 Halogen bonds: C:A.53 YMZ.22: 16 residues within 4Å: Chain D: W.33, F.37, F.44, D.46, F.47, G.49, S.52, A.53, W.56, R.57, V.60, L.83, M.85, S.103, F.104, F.422 7 PLIP interactions: 7 interactions with chain D Hydrophobic interactions: D:F.44, D:W.56, D:W.56, D:L.83 Hydrogen bonds: D:W.56 Water bridges: D:F.422 Halogen bonds: D:A.53 YMZ.29: 16 residues within 4Å: Chain E: W.33, F.37, F.44, D.46, F.47, G.49, S.52, A.53, W.56, R.57, V.60, L.83, M.85, S.103, F.104, F.422 7 PLIP interactions: 7 interactions with chain E Hydrophobic interactions: E:F.44, E:W.56, E:W.56, E:L.83 Hydrogen bonds: E:W.56 Water bridges: E:F.422 Halogen bonds: E:A.53 YMZ.36: 16 residues within 4Å: Chain F: W.33, F.37, F.44, D.46, F.47, G.49, S.52, A.53, W.56, R.57, V.60, L.83, M.85, S.103, F.104, F.422 7 PLIP interactions: 7 interactions with chain F Hydrophobic interactions: F:F.44, F:W.56, F:W.56, F:L.83 Hydrogen bonds: F:W.56 Water bridges: F:F.422 Halogen bonds: F:A.53

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

DMS.2: 6 residues within 4Å: Chain A: G.93, G.329, Y.330, A.331, A.411, D.413 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.413 Water bridges: A:V.414 DMS.9: 6 residues within 4Å: Chain B: G.93, G.329, Y.330, A.331, A.411, D.413 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.413 Water bridges: B:V.414 DMS.16: 6 residues within 4Å: Chain C: G.93, G.329, Y.330, A.331, A.411, D.413 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:D.413 Water bridges: C:V.414 DMS.23: 6 residues within 4Å: Chain D: G.93, G.329, Y.330, A.331, A.411, D.413 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:D.413 Water bridges: D:V.414 DMS.30: 6 residues within 4Å: Chain E: G.93, G.329, Y.330, A.331, A.411, D.413 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:D.413 Water bridges: E:V.414 DMS.37: 6 residues within 4Å: Chain F: G.93, G.329, Y.330, A.331, A.411, D.413 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:D.413 Water bridges: F:V.414

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

PEG.3: 3 residues within 4Å: Chain A: N.393, R.396 Chain E: D.172 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain E Hydrogen bonds: A:N.393, E:D.172 PEG.4: 9 residues within 4Å: Chain A: L.261, H.269, I.287, T.289, H.290, D.293, P.294, Q.417 Ligands: GOL.6 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.289, A:T.289 Water bridges: A:L.261 PEG.10: 3 residues within 4Å: Chain B: N.393, R.396 Chain D: D.172 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain D Hydrogen bonds: B:N.393, D:D.172 PEG.11: 9 residues within 4Å: Chain B: L.261, H.269, I.287, T.289, H.290, D.293, P.294, Q.417 Ligands: GOL.13 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.289, B:T.289 Water bridges: B:L.261 PEG.17: 3 residues within 4Å: Chain C: N.393, R.396 Chain F: D.172 2 PLIP interactions: 1 interactions with chain F, 1 interactions with chain C Hydrogen bonds: F:D.172, C:N.393 PEG.18: 9 residues within 4Å: Chain C: L.261, H.269, I.287, T.289, H.290, D.293, P.294, Q.417 Ligands: GOL.20 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:T.289, C:T.289 Water bridges: C:L.261 PEG.24: 3 residues within 4Å: Chain B: D.172 Chain D: N.393, R.396 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.393 PEG.25: 9 residues within 4Å: Chain D: L.261, H.269, I.287, T.289, H.290, D.293, P.294, Q.417 Ligands: GOL.27 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:T.289 Water bridges: D:L.261 PEG.31: 3 residues within 4Å: Chain A: D.172 Chain E: N.393, R.396 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:N.393 PEG.32: 9 residues within 4Å: Chain E: L.261, H.269, I.287, T.289, H.290, D.293, P.294, Q.417 Ligands: GOL.34 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:T.289 Water bridges: E:L.261 PEG.38: 3 residues within 4Å: Chain C: D.172 Chain F: N.393, R.396 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:N.393 PEG.39: 9 residues within 4Å: Chain F: L.261, H.269, I.287, T.289, H.290, D.293, P.294, Q.417 Ligands: GOL.41 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:T.289 Water bridges: F:L.261

18 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 6 residues within 4Å: Chain A: P.28, R.57, V.60, P.61, T.62, A.65 Ligand excluded by PLIP GOL.6: 8 residues within 4Å: Chain A: L.157, R.262, I.288, T.289, H.290, Q.417, T.418 Ligands: PEG.4 Ligand excluded by PLIP GOL.7: 6 residues within 4Å: Chain A: H.125, R.126, A.129, R.317, M.319, R.373 Ligand excluded by PLIP GOL.12: 6 residues within 4Å: Chain B: P.28, R.57, V.60, P.61, T.62, A.65 Ligand excluded by PLIP GOL.13: 8 residues within 4Å: Chain B: L.157, R.262, I.288, T.289, H.290, Q.417, T.418 Ligands: PEG.11 Ligand excluded by PLIP GOL.14: 6 residues within 4Å: Chain B: H.125, R.126, A.129, R.317, M.319, R.373 Ligand excluded by PLIP GOL.19: 6 residues within 4Å: Chain C: P.28, R.57, V.60, P.61, T.62, A.65 Ligand excluded by PLIP GOL.20: 8 residues within 4Å: Chain C: L.157, R.262, I.288, T.289, H.290, Q.417, T.418 Ligands: PEG.18 Ligand excluded by PLIP GOL.21: 6 residues within 4Å: Chain C: H.125, R.126, A.129, R.317, M.319, R.373 Ligand excluded by PLIP GOL.26: 6 residues within 4Å: Chain D: P.28, R.57, V.60, P.61, T.62, A.65 Ligand excluded by PLIP GOL.27: 8 residues within 4Å: Chain D: L.157, R.262, I.288, T.289, H.290, Q.417, T.418 Ligands: PEG.25 Ligand excluded by PLIP GOL.28: 6 residues within 4Å: Chain D: H.125, R.126, A.129, R.317, M.319, R.373 Ligand excluded by PLIP GOL.33: 6 residues within 4Å: Chain E: P.28, R.57, V.60, P.61, T.62, A.65 Ligand excluded by PLIP GOL.34: 8 residues within 4Å: Chain E: L.157, R.262, I.288, T.289, H.290, Q.417, T.418 Ligands: PEG.32 Ligand excluded by PLIP GOL.35: 6 residues within 4Å: Chain E: H.125, R.126, A.129, R.317, M.319, R.373 Ligand excluded by PLIP GOL.40: 6 residues within 4Å: Chain F: P.28, R.57, V.60, P.61, T.62, A.65 Ligand excluded by PLIP GOL.41: 8 residues within 4Å: Chain F: L.157, R.262, I.288, T.289, H.290, Q.417, T.418 Ligands: PEG.39 Ligand excluded by PLIP GOL.42: 6 residues within 4Å: Chain F: H.125, R.126, A.129, R.317, M.319, R.373 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pang, A.H. et al., Discovery and Mechanistic Analysis of Structurally Diverse Inhibitors of Acetyltransferase Eis among FDA-Approved Drugs. Biochemistry (2023)

Release Date

2023-02-01

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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