SMTL ID : 8f58.1

Crystal structure of acetyltransferase Eis from M. tuberculosis in complex with inhibitor SGT1616

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-hexamer

Ligands

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

DMS.1: 2 residues within 4Å: Chain A: E.159, R.257 Ligand excluded by PLIP DMS.2: 8 residues within 4Å: Chain A: R.262, I.288, T.289, H.290, Q.417, T.418 Ligands: GOL.4, PEG.8 Ligand excluded by PLIP DMS.3: 8 residues within 4Å: Chain A: P.92, G.93, R.328, G.329, Y.330, A.331, A.411, D.413 Ligand excluded by PLIP DMS.9: 2 residues within 4Å: Chain B: E.159, R.257 Ligand excluded by PLIP DMS.10: 8 residues within 4Å: Chain B: R.262, I.288, T.289, H.290, Q.417, T.418 Ligands: GOL.12, PEG.16 Ligand excluded by PLIP DMS.11: 8 residues within 4Å: Chain B: P.92, G.93, R.328, G.329, Y.330, A.331, A.411, D.413 Ligand excluded by PLIP DMS.17: 2 residues within 4Å: Chain C: E.159, R.257 Ligand excluded by PLIP DMS.18: 8 residues within 4Å: Chain C: R.262, I.288, T.289, H.290, Q.417, T.418 Ligands: GOL.20, PEG.24 Ligand excluded by PLIP DMS.19: 8 residues within 4Å: Chain C: P.92, G.93, R.328, G.329, Y.330, A.331, A.411, D.413 Ligand excluded by PLIP DMS.25: 2 residues within 4Å: Chain D: E.159, R.257 Ligand excluded by PLIP DMS.26: 8 residues within 4Å: Chain D: R.262, I.288, T.289, H.290, Q.417, T.418 Ligands: GOL.28, PEG.32 Ligand excluded by PLIP DMS.27: 8 residues within 4Å: Chain D: P.92, G.93, R.328, G.329, Y.330, A.331, A.411, D.413 Ligand excluded by PLIP DMS.33: 2 residues within 4Å: Chain E: E.159, R.257 Ligand excluded by PLIP DMS.34: 8 residues within 4Å: Chain E: R.262, I.288, T.289, H.290, Q.417, T.418 Ligands: GOL.36, PEG.40 Ligand excluded by PLIP DMS.35: 8 residues within 4Å: Chain E: P.92, G.93, R.328, G.329, Y.330, A.331, A.411, D.413 Ligand excluded by PLIP DMS.41: 2 residues within 4Å: Chain F: E.159, R.257 Ligand excluded by PLIP DMS.42: 8 residues within 4Å: Chain F: R.262, I.288, T.289, H.290, Q.417, T.418 Ligands: GOL.44, PEG.48 Ligand excluded by PLIP DMS.43: 8 residues within 4Å: Chain F: P.92, G.93, R.328, G.329, Y.330, A.331, A.411, D.413 Ligand excluded by PLIP

18 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 5 residues within 4Å: Chain A: I.288, T.418, A.419, E.421 Ligands: DMS.2 Ligand excluded by PLIP GOL.6: 7 residues within 4Å: Chain A: S.103, F.104, V.105, H.139, A.140, S.141, Y.146 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: 5 residues within 4Å: Chain B: I.288, T.418, A.419, E.421 Ligands: DMS.10 Ligand excluded by PLIP GOL.14: 7 residues within 4Å: Chain B: S.103, F.104, V.105, H.139, A.140, S.141, Y.146 Ligand excluded by PLIP GOL.15: 6 residues within 4Å: Chain B: H.125, R.126, A.129, R.317, M.319, R.373 Ligand excluded by PLIP GOL.20: 5 residues within 4Å: Chain C: I.288, T.418, A.419, E.421 Ligands: DMS.18 Ligand excluded by PLIP GOL.22: 7 residues within 4Å: Chain C: S.103, F.104, V.105, H.139, A.140, S.141, Y.146 Ligand excluded by PLIP GOL.23: 6 residues within 4Å: Chain C: H.125, R.126, A.129, R.317, M.319, R.373 Ligand excluded by PLIP GOL.28: 5 residues within 4Å: Chain D: I.288, T.418, A.419, E.421 Ligands: DMS.26 Ligand excluded by PLIP GOL.30: 7 residues within 4Å: Chain D: S.103, F.104, V.105, H.139, A.140, S.141, Y.146 Ligand excluded by PLIP GOL.31: 6 residues within 4Å: Chain D: H.125, R.126, A.129, R.317, M.319, R.373 Ligand excluded by PLIP GOL.36: 5 residues within 4Å: Chain E: I.288, T.418, A.419, E.421 Ligands: DMS.34 Ligand excluded by PLIP GOL.38: 7 residues within 4Å: Chain E: S.103, F.104, V.105, H.139, A.140, S.141, Y.146 Ligand excluded by PLIP GOL.39: 6 residues within 4Å: Chain E: H.125, R.126, A.129, R.317, M.319, R.373 Ligand excluded by PLIP GOL.44: 5 residues within 4Å: Chain F: I.288, T.418, A.419, E.421 Ligands: DMS.42 Ligand excluded by PLIP GOL.46: 7 residues within 4Å: Chain F: S.103, F.104, V.105, H.139, A.140, S.141, Y.146 Ligand excluded by PLIP GOL.47: 6 residues within 4Å: Chain F: H.125, R.126, A.129, R.317, M.319, R.373 Ligand excluded by PLIP

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

XEH.5: 11 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 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:I.48, A:A.53, A:W.56, A:W.56, A:V.60, A:L.83, A:L.83, A:F.104, A:F.104 Hydrogen bonds: A:S.103, A:S.103 XEH.13: 11 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 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:I.48, B:A.53, B:W.56, B:W.56, B:V.60, B:L.83, B:L.83, B:F.104, B:F.104 Hydrogen bonds: B:S.103, B:S.103 XEH.21: 11 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 11 PLIP interactions: 11 interactions with chain C Hydrophobic interactions: C:I.48, C:A.53, C:W.56, C:W.56, C:V.60, C:L.83, C:L.83, C:F.104, C:F.104 Hydrogen bonds: C:S.103, C:S.103 XEH.29: 11 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 12 PLIP interactions: 12 interactions with chain D Hydrophobic interactions: D:I.48, D:A.53, D:W.56, D:W.56, D:V.60, D:L.83, D:L.83, D:F.104, D:F.104 Hydrogen bonds: D:S.103, D:S.103, D:F.422 XEH.37: 11 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 12 PLIP interactions: 12 interactions with chain E Hydrophobic interactions: E:I.48, E:A.53, E:W.56, E:W.56, E:V.60, E:L.83, E:L.83, E:F.104, E:F.104 Hydrogen bonds: E:S.103, E:S.103, E:F.422 XEH.45: 11 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 12 PLIP interactions: 12 interactions with chain F Hydrophobic interactions: F:I.48, F:A.53, F:W.56, F:W.56, F:V.60, F:L.83, F:L.83, F:F.104, F:F.104 Hydrogen bonds: F:S.103, F:S.103, F:F.422

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

PEG.8: 10 residues within 4Å: Chain A: L.261, H.269, I.287, I.288, T.289, H.290, D.293, P.294, Q.417 Ligands: DMS.2 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:I.288, A:T.289 PEG.16: 10 residues within 4Å: Chain B: L.261, H.269, I.287, I.288, T.289, H.290, D.293, P.294, Q.417 Ligands: DMS.10 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:I.288, B:T.289 PEG.24: 10 residues within 4Å: Chain C: L.261, H.269, I.287, I.288, T.289, H.290, D.293, P.294, Q.417 Ligands: DMS.18 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:I.288, C:T.289 PEG.32: 10 residues within 4Å: Chain D: L.261, H.269, I.287, I.288, T.289, H.290, D.293, P.294, Q.417 Ligands: DMS.26 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:I.288 PEG.40: 10 residues within 4Å: Chain E: L.261, H.269, I.287, I.288, T.289, H.290, D.293, P.294, Q.417 Ligands: DMS.34 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:I.288 PEG.48: 10 residues within 4Å: Chain F: L.261, H.269, I.287, I.288, T.289, H.290, D.293, P.294, Q.417 Ligands: DMS.42 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:I.288

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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