SMTL ID : 8f57.1

Crystal structure of acetyltransferase Eis from M. tuberculosis in complex with inhibitor SGT1615

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.42 Å

Oligo State

homo-hexamer

Ligands

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

DMS.1: 7 residues within 4Å: Chain A: R.262, I.288, T.289, H.290, Q.417, T.418 Ligands: DMS.6 Ligand excluded by PLIP DMS.4: 7 residues within 4Å: Chain A: P.92, G.93, Y.330, A.331, A.411, S.412, D.413 Ligand excluded by PLIP DMS.5: 8 residues within 4Å: Chain A: W.33, R.57, V.60, P.61, T.62, D.63, G.64, A.65 Ligand excluded by PLIP DMS.6: 7 residues within 4Å: Chain A: L.157, I.288, T.418, A.419, F.420, E.421 Ligands: DMS.1 Ligand excluded by PLIP DMS.7: 6 residues within 4Å: Chain A: A.367, E.368, E.370, R.396, T.397, K.398 Ligand excluded by PLIP DMS.11: 7 residues within 4Å: Chain B: R.262, I.288, T.289, H.290, Q.417, T.418 Ligands: DMS.16 Ligand excluded by PLIP DMS.14: 7 residues within 4Å: Chain B: P.92, G.93, Y.330, A.331, A.411, S.412, D.413 Ligand excluded by PLIP DMS.15: 8 residues within 4Å: Chain B: W.33, R.57, V.60, P.61, T.62, D.63, G.64, A.65 Ligand excluded by PLIP DMS.16: 7 residues within 4Å: Chain B: L.157, I.288, T.418, A.419, F.420, E.421 Ligands: DMS.11 Ligand excluded by PLIP DMS.17: 6 residues within 4Å: Chain B: A.367, E.368, E.370, R.396, T.397, K.398 Ligand excluded by PLIP DMS.21: 7 residues within 4Å: Chain C: R.262, I.288, T.289, H.290, Q.417, T.418 Ligands: DMS.26 Ligand excluded by PLIP DMS.24: 7 residues within 4Å: Chain C: P.92, G.93, Y.330, A.331, A.411, S.412, D.413 Ligand excluded by PLIP DMS.25: 8 residues within 4Å: Chain C: W.33, R.57, V.60, P.61, T.62, D.63, G.64, A.65 Ligand excluded by PLIP DMS.26: 7 residues within 4Å: Chain C: L.157, I.288, T.418, A.419, F.420, E.421 Ligands: DMS.21 Ligand excluded by PLIP DMS.27: 6 residues within 4Å: Chain C: A.367, E.368, E.370, R.396, T.397, K.398 Ligand excluded by PLIP DMS.31: 7 residues within 4Å: Chain D: R.262, I.288, T.289, H.290, Q.417, T.418 Ligands: DMS.36 Ligand excluded by PLIP DMS.34: 7 residues within 4Å: Chain D: P.92, G.93, Y.330, A.331, A.411, S.412, D.413 Ligand excluded by PLIP DMS.35: 8 residues within 4Å: Chain D: W.33, R.57, V.60, P.61, T.62, D.63, G.64, A.65 Ligand excluded by PLIP DMS.36: 7 residues within 4Å: Chain D: L.157, I.288, T.418, A.419, F.420, E.421 Ligands: DMS.31 Ligand excluded by PLIP DMS.37: 6 residues within 4Å: Chain D: A.367, E.368, E.370, R.396, T.397, K.398 Ligand excluded by PLIP DMS.41: 7 residues within 4Å: Chain E: R.262, I.288, T.289, H.290, Q.417, T.418 Ligands: DMS.46 Ligand excluded by PLIP DMS.44: 7 residues within 4Å: Chain E: P.92, G.93, Y.330, A.331, A.411, S.412, D.413 Ligand excluded by PLIP DMS.45: 8 residues within 4Å: Chain E: W.33, R.57, V.60, P.61, T.62, D.63, G.64, A.65 Ligand excluded by PLIP DMS.46: 7 residues within 4Å: Chain E: L.157, I.288, T.418, A.419, F.420, E.421 Ligands: DMS.41 Ligand excluded by PLIP DMS.47: 6 residues within 4Å: Chain E: A.367, E.368, E.370, R.396, T.397, K.398 Ligand excluded by PLIP DMS.51: 7 residues within 4Å: Chain F: R.262, I.288, T.289, H.290, Q.417, T.418 Ligands: DMS.56 Ligand excluded by PLIP DMS.54: 7 residues within 4Å: Chain F: P.92, G.93, Y.330, A.331, A.411, S.412, D.413 Ligand excluded by PLIP DMS.55: 8 residues within 4Å: Chain F: W.33, R.57, V.60, P.61, T.62, D.63, G.64, A.65 Ligand excluded by PLIP DMS.56: 7 residues within 4Å: Chain F: L.157, I.288, T.418, A.419, F.420, E.421 Ligands: DMS.51 Ligand excluded by PLIP DMS.57: 6 residues within 4Å: Chain F: A.367, E.368, E.370, R.396, T.397, K.398 Ligand excluded by PLIP

6 x XEL: (1E)-1-[(4-chlorophenyl)methylidene]-2-(3-fluorophenyl)hydrazine(Non-covalent)

XEL.2: 12 residues within 4Å: Chain A: W.33, I.48, A.53, W.56, R.57, V.60, L.83, M.85, S.103, F.104, F.422 Ligands: GOL.10 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:I.48, A:W.56, A:W.56, A:V.60, A:L.83, A:L.83, A:F.104 Hydrogen bonds: A:S.103 XEL.12: 12 residues within 4Å: Chain B: W.33, I.48, A.53, W.56, R.57, V.60, L.83, M.85, S.103, F.104, F.422 Ligands: GOL.20 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:I.48, B:W.56, B:W.56, B:V.60, B:L.83, B:L.83, B:F.104 Hydrogen bonds: B:S.103 XEL.22: 12 residues within 4Å: Chain C: W.33, I.48, A.53, W.56, R.57, V.60, L.83, M.85, S.103, F.104, F.422 Ligands: GOL.30 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: C:I.48, C:W.56, C:W.56, C:V.60, C:L.83, C:L.83, C:F.104 Hydrogen bonds: C:S.103 XEL.32: 12 residues within 4Å: Chain D: W.33, I.48, A.53, W.56, R.57, V.60, L.83, M.85, S.103, F.104, F.422 Ligands: GOL.40 8 PLIP interactions: 8 interactions with chain D Hydrophobic interactions: D:I.48, D:W.56, D:W.56, D:V.60, D:L.83, D:L.83, D:F.104 Hydrogen bonds: D:S.103 XEL.42: 12 residues within 4Å: Chain E: W.33, I.48, A.53, W.56, R.57, V.60, L.83, M.85, S.103, F.104, F.422 Ligands: GOL.50 8 PLIP interactions: 8 interactions with chain E Hydrophobic interactions: E:I.48, E:W.56, E:W.56, E:V.60, E:L.83, E:L.83, E:F.104 Hydrogen bonds: E:S.103 XEL.52: 12 residues within 4Å: Chain F: W.33, I.48, A.53, W.56, R.57, V.60, L.83, M.85, S.103, F.104, F.422 Ligands: GOL.60 8 PLIP interactions: 8 interactions with chain F Hydrophobic interactions: F:I.48, F:W.56, F:W.56, F:V.60, F:L.83, F:L.83, F:F.104 Hydrogen bonds: F:S.103

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

PEG.3: 9 residues within 4Å: Chain A: W.202, L.261, R.262, A.263, H.269, H.290, D.293, P.294, Q.417 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:W.202, A:A.263 Water bridges: A:T.289 PEG.13: 9 residues within 4Å: Chain B: W.202, L.261, R.262, A.263, H.269, H.290, D.293, P.294, Q.417 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:W.202, B:A.263 Water bridges: B:T.289 PEG.23: 9 residues within 4Å: Chain C: W.202, L.261, R.262, A.263, H.269, H.290, D.293, P.294, Q.417 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:W.202, C:A.263 Water bridges: C:T.289 PEG.33: 9 residues within 4Å: Chain D: W.202, L.261, R.262, A.263, H.269, H.290, D.293, P.294, Q.417 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:W.202, D:A.263 PEG.43: 9 residues within 4Å: Chain E: W.202, L.261, R.262, A.263, H.269, H.290, D.293, P.294, Q.417 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:W.202, E:A.263 PEG.53: 9 residues within 4Å: Chain F: W.202, L.261, R.262, A.263, H.269, H.290, D.293, P.294, Q.417 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:W.202, F:A.263

18 x GOL: GLYCEROL(Non-functional Binders)

GOL.8: 9 residues within 4Å: Chain A: F.44, S.103, F.104, V.105, H.139, A.140, S.141, Y.146 Ligands: GOL.10 Ligand excluded by PLIP GOL.9: 5 residues within 4Å: Chain A: H.125, R.126, R.317, M.319, R.373 Ligand excluded by PLIP GOL.10: 7 residues within 4Å: Chain A: F.44, D.46, F.47, S.103, F.104 Ligands: XEL.2, GOL.8 Ligand excluded by PLIP GOL.18: 9 residues within 4Å: Chain B: F.44, S.103, F.104, V.105, H.139, A.140, S.141, Y.146 Ligands: GOL.20 Ligand excluded by PLIP GOL.19: 5 residues within 4Å: Chain B: H.125, R.126, R.317, M.319, R.373 Ligand excluded by PLIP GOL.20: 7 residues within 4Å: Chain B: F.44, D.46, F.47, S.103, F.104 Ligands: XEL.12, GOL.18 Ligand excluded by PLIP GOL.28: 9 residues within 4Å: Chain C: F.44, S.103, F.104, V.105, H.139, A.140, S.141, Y.146 Ligands: GOL.30 Ligand excluded by PLIP GOL.29: 5 residues within 4Å: Chain C: H.125, R.126, R.317, M.319, R.373 Ligand excluded by PLIP GOL.30: 7 residues within 4Å: Chain C: F.44, D.46, F.47, S.103, F.104 Ligands: XEL.22, GOL.28 Ligand excluded by PLIP GOL.38: 9 residues within 4Å: Chain D: F.44, S.103, F.104, V.105, H.139, A.140, S.141, Y.146 Ligands: GOL.40 Ligand excluded by PLIP GOL.39: 5 residues within 4Å: Chain D: H.125, R.126, R.317, M.319, R.373 Ligand excluded by PLIP GOL.40: 7 residues within 4Å: Chain D: F.44, D.46, F.47, S.103, F.104 Ligands: XEL.32, GOL.38 Ligand excluded by PLIP GOL.48: 9 residues within 4Å: Chain E: F.44, S.103, F.104, V.105, H.139, A.140, S.141, Y.146 Ligands: GOL.50 Ligand excluded by PLIP GOL.49: 5 residues within 4Å: Chain E: H.125, R.126, R.317, M.319, R.373 Ligand excluded by PLIP GOL.50: 7 residues within 4Å: Chain E: F.44, D.46, F.47, S.103, F.104 Ligands: XEL.42, GOL.48 Ligand excluded by PLIP GOL.58: 9 residues within 4Å: Chain F: F.44, S.103, F.104, V.105, H.139, A.140, S.141, Y.146 Ligands: GOL.60 Ligand excluded by PLIP GOL.59: 5 residues within 4Å: Chain F: H.125, R.126, R.317, M.319, R.373 Ligand excluded by PLIP GOL.60: 7 residues within 4Å: Chain F: F.44, D.46, F.47, S.103, F.104 Ligands: XEL.52, GOL.58 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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