SMTL ID : 8f4w.1

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-hexamer

Ligands

6 x VFX: 1-[(1R)-2-(dimethylamino)-1-(4-methoxyphenyl)ethyl]cyclohexan-1-ol(Non-covalent)

VFX.1: 10 residues within 4Å: Chain A: F.44, D.46, A.53, W.56, R.57, L.83, S.103, F.104, E.421, F.422 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.44, A:A.53, A:W.56, A:F.104 pi-Stacking: A:W.56 VFX.12: 10 residues within 4Å: Chain B: F.44, D.46, A.53, W.56, R.57, L.83, S.103, F.104, E.421, F.422 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:F.44, B:A.53, B:W.56, B:F.104 pi-Stacking: B:W.56 VFX.23: 10 residues within 4Å: Chain C: F.44, D.46, A.53, W.56, R.57, L.83, S.103, F.104, E.421, F.422 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:F.44, C:A.53, C:W.56, C:F.104 pi-Stacking: C:W.56 VFX.34: 10 residues within 4Å: Chain D: F.44, D.46, A.53, W.56, R.57, L.83, S.103, F.104, E.421, F.422 5 PLIP interactions: 5 interactions with chain D Hydrophobic interactions: D:F.44, D:A.53, D:W.56, D:F.104 pi-Stacking: D:W.56 VFX.45: 10 residues within 4Å: Chain E: F.44, D.46, A.53, W.56, R.57, L.83, S.103, F.104, E.421, F.422 5 PLIP interactions: 5 interactions with chain E Hydrophobic interactions: E:F.44, E:A.53, E:W.56, E:F.104 pi-Stacking: E:W.56 VFX.56: 10 residues within 4Å: Chain F: F.44, D.46, A.53, W.56, R.57, L.83, S.103, F.104, E.421, F.422 5 PLIP interactions: 5 interactions with chain F Hydrophobic interactions: F:F.44, F:A.53, F:W.56, F:F.104 pi-Stacking: F:W.56

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

DMS.2: 8 residues within 4Å: Chain A: P.92, R.328, G.329, Y.330, A.331, A.411, D.413 Ligands: GOL.3 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.413 DMS.13: 8 residues within 4Å: Chain B: P.92, R.328, G.329, Y.330, A.331, A.411, D.413 Ligands: GOL.14 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.413 DMS.24: 8 residues within 4Å: Chain C: P.92, R.328, G.329, Y.330, A.331, A.411, D.413 Ligands: GOL.25 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:D.413 DMS.35: 8 residues within 4Å: Chain D: P.92, R.328, G.329, Y.330, A.331, A.411, D.413 Ligands: GOL.36 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:D.413 Water bridges: D:H.332, D:H.332 DMS.46: 8 residues within 4Å: Chain E: P.92, R.328, G.329, Y.330, A.331, A.411, D.413 Ligands: GOL.47 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:D.413 Water bridges: E:H.332, E:H.332 DMS.57: 8 residues within 4Å: Chain F: P.92, R.328, G.329, Y.330, A.331, A.411, D.413 Ligands: GOL.58 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:D.413 Water bridges: F:H.332, F:H.332

42 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 9 residues within 4Å: Chain A: V.91, P.92, G.93, E.94, P.207, S.412, D.413, V.414 Ligands: DMS.2 Ligand excluded by PLIP GOL.4: 7 residues within 4Å: Chain A: A.263, T.265, A.266, H.269, P.294 Chain E: A.391 Ligands: PEG.5 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.5 Ligand excluded by PLIP GOL.7: 5 residues within 4Å: Chain A: H.125, A.129, R.317, M.319, R.373 Ligand excluded by PLIP GOL.9: 6 residues within 4Å: Chain A: R.57, V.60, P.61, T.62, D.63, A.65 Ligand excluded by PLIP GOL.10: 8 residues within 4Å: Chain A: F.44, S.103, F.104, V.105, H.139, S.141, Y.146, F.422 Ligand excluded by PLIP GOL.11: 6 residues within 4Å: Chain A: A.367, E.368, E.370, R.396, T.397, K.398 Ligand excluded by PLIP GOL.14: 9 residues within 4Å: Chain B: V.91, P.92, G.93, E.94, P.207, S.412, D.413, V.414 Ligands: DMS.13 Ligand excluded by PLIP GOL.15: 7 residues within 4Å: Chain B: A.263, T.265, A.266, H.269, P.294 Chain D: A.391 Ligands: PEG.16 Ligand excluded by PLIP GOL.17: 8 residues within 4Å: Chain B: L.157, R.262, I.288, T.289, H.290, Q.417, T.418 Ligands: PEG.16 Ligand excluded by PLIP GOL.18: 5 residues within 4Å: Chain B: H.125, A.129, R.317, M.319, R.373 Ligand excluded by PLIP GOL.20: 6 residues within 4Å: Chain B: R.57, V.60, P.61, T.62, D.63, A.65 Ligand excluded by PLIP GOL.21: 8 residues within 4Å: Chain B: F.44, S.103, F.104, V.105, H.139, S.141, Y.146, F.422 Ligand excluded by PLIP GOL.22: 6 residues within 4Å: Chain B: A.367, E.368, E.370, R.396, T.397, K.398 Ligand excluded by PLIP GOL.25: 9 residues within 4Å: Chain C: V.91, P.92, G.93, E.94, P.207, S.412, D.413, V.414 Ligands: DMS.24 Ligand excluded by PLIP GOL.26: 7 residues within 4Å: Chain C: A.263, T.265, A.266, H.269, P.294 Chain F: A.391 Ligands: PEG.27 Ligand excluded by PLIP GOL.28: 8 residues within 4Å: Chain C: L.157, R.262, I.288, T.289, H.290, Q.417, T.418 Ligands: PEG.27 Ligand excluded by PLIP GOL.29: 5 residues within 4Å: Chain C: H.125, A.129, R.317, M.319, R.373 Ligand excluded by PLIP GOL.31: 6 residues within 4Å: Chain C: R.57, V.60, P.61, T.62, D.63, A.65 Ligand excluded by PLIP GOL.32: 8 residues within 4Å: Chain C: F.44, S.103, F.104, V.105, H.139, S.141, Y.146, F.422 Ligand excluded by PLIP GOL.33: 6 residues within 4Å: Chain C: A.367, E.368, E.370, R.396, T.397, K.398 Ligand excluded by PLIP GOL.36: 9 residues within 4Å: Chain D: V.91, P.92, G.93, E.94, P.207, S.412, D.413, V.414 Ligands: DMS.35 Ligand excluded by PLIP GOL.37: 7 residues within 4Å: Chain B: A.391 Chain D: A.263, T.265, A.266, H.269, P.294 Ligands: PEG.38 Ligand excluded by PLIP GOL.39: 8 residues within 4Å: Chain D: L.157, R.262, I.288, T.289, H.290, Q.417, T.418 Ligands: PEG.38 Ligand excluded by PLIP GOL.40: 5 residues within 4Å: Chain D: H.125, A.129, R.317, M.319, R.373 Ligand excluded by PLIP GOL.42: 6 residues within 4Å: Chain D: R.57, V.60, P.61, T.62, D.63, A.65 Ligand excluded by PLIP GOL.43: 8 residues within 4Å: Chain D: F.44, S.103, F.104, V.105, H.139, S.141, Y.146, F.422 Ligand excluded by PLIP GOL.44: 6 residues within 4Å: Chain D: A.367, E.368, E.370, R.396, T.397, K.398 Ligand excluded by PLIP GOL.47: 9 residues within 4Å: Chain E: V.91, P.92, G.93, E.94, P.207, S.412, D.413, V.414 Ligands: DMS.46 Ligand excluded by PLIP GOL.48: 7 residues within 4Å: Chain A: A.391 Chain E: A.263, T.265, A.266, H.269, P.294 Ligands: PEG.49 Ligand excluded by PLIP GOL.50: 8 residues within 4Å: Chain E: L.157, R.262, I.288, T.289, H.290, Q.417, T.418 Ligands: PEG.49 Ligand excluded by PLIP GOL.51: 5 residues within 4Å: Chain E: H.125, A.129, R.317, M.319, R.373 Ligand excluded by PLIP GOL.53: 6 residues within 4Å: Chain E: R.57, V.60, P.61, T.62, D.63, A.65 Ligand excluded by PLIP GOL.54: 8 residues within 4Å: Chain E: F.44, S.103, F.104, V.105, H.139, S.141, Y.146, F.422 Ligand excluded by PLIP GOL.55: 6 residues within 4Å: Chain E: A.367, E.368, E.370, R.396, T.397, K.398 Ligand excluded by PLIP GOL.58: 9 residues within 4Å: Chain F: V.91, P.92, G.93, E.94, P.207, S.412, D.413, V.414 Ligands: DMS.57 Ligand excluded by PLIP GOL.59: 7 residues within 4Å: Chain C: A.391 Chain F: A.263, T.265, A.266, H.269, P.294 Ligands: PEG.60 Ligand excluded by PLIP GOL.61: 8 residues within 4Å: Chain F: L.157, R.262, I.288, T.289, H.290, Q.417, T.418 Ligands: PEG.60 Ligand excluded by PLIP GOL.62: 5 residues within 4Å: Chain F: H.125, A.129, R.317, M.319, R.373 Ligand excluded by PLIP GOL.64: 6 residues within 4Å: Chain F: R.57, V.60, P.61, T.62, D.63, A.65 Ligand excluded by PLIP GOL.65: 8 residues within 4Å: Chain F: F.44, S.103, F.104, V.105, H.139, S.141, Y.146, F.422 Ligand excluded by PLIP GOL.66: 6 residues within 4Å: Chain F: A.367, E.368, E.370, R.396, T.397, K.398 Ligand excluded by PLIP

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

PEG.5: 10 residues within 4Å: Chain A: L.261, H.269, I.287, T.289, H.290, D.293, P.294, Q.417 Ligands: GOL.4, GOL.6 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.289 Water bridges: A:L.261, A:I.288 PEG.8: 5 residues within 4Å: Chain A: T.58, L.59, V.60, P.61, D.86 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.59 Water bridges: A:R.57, A:T.58 PEG.16: 10 residues within 4Å: Chain B: L.261, H.269, I.287, T.289, H.290, D.293, P.294, Q.417 Ligands: GOL.15, GOL.17 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.289 Water bridges: B:L.261, B:I.288 PEG.19: 5 residues within 4Å: Chain B: T.58, L.59, V.60, P.61, D.86 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:L.59 Water bridges: B:R.57, B:T.58 PEG.27: 10 residues within 4Å: Chain C: L.261, H.269, I.287, T.289, H.290, D.293, P.294, Q.417 Ligands: GOL.26, GOL.28 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:T.289 Water bridges: C:L.261, C:I.288 PEG.30: 5 residues within 4Å: Chain C: T.58, L.59, V.60, P.61, D.86 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:L.59 Water bridges: C:R.57, C:T.58 PEG.38: 10 residues within 4Å: Chain D: L.261, H.269, I.287, T.289, H.290, D.293, P.294, Q.417 Ligands: GOL.37, GOL.39 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:D.293 Water bridges: D:L.261, D:I.288 PEG.41: 5 residues within 4Å: Chain D: T.58, L.59, V.60, P.61, D.86 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:L.59 Water bridges: D:R.57, D:T.58, D:D.86 PEG.49: 10 residues within 4Å: Chain E: L.261, H.269, I.287, T.289, H.290, D.293, P.294, Q.417 Ligands: GOL.48, GOL.50 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:D.293 Water bridges: E:L.261, E:I.288 PEG.52: 5 residues within 4Å: Chain E: T.58, L.59, V.60, P.61, D.86 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:L.59 Water bridges: E:R.57, E:T.58, E:D.86 PEG.60: 10 residues within 4Å: Chain F: L.261, H.269, I.287, T.289, H.290, D.293, P.294, Q.417 Ligands: GOL.59, GOL.61 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:D.293 Water bridges: F:L.261, F:I.288 PEG.63: 5 residues within 4Å: Chain F: T.58, L.59, V.60, P.61, D.86 4 PLIP interactions: 4 interactions with chain F Hydrogen bonds: F:L.59 Water bridges: F:R.57, F:T.58, F:D.86

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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