SMTL ID : 6x6g.1

Crystal structure of acetyltransferase Eis from Mycobacterium tuberculosis in complex with droperidol

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.15 Å

Oligo State

homo-hexamer

Ligands

6 x USS: 3-[1-[4-(4-fluorophenyl)-4-oxidanylidene-butyl]-2,3,4,5-tetrahydropyridin-4-yl]-1~{H}-benzimidazol-2-one(Non-covalent)

USS.1: 15 residues within 4Å: Chain A: W.33, D.46, I.48, A.53, W.56, R.57, V.60, L.83, M.85, S.103, F.104, E.223, E.421, F.422 Ligands: GOL.9 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:A.53, A:W.56, A:W.56, A:L.83, A:F.104, A:E.421 Salt bridges: A:D.46 USS.10: 15 residues within 4Å: Chain B: W.33, D.46, I.48, A.53, W.56, R.57, V.60, L.83, M.85, S.103, F.104, E.223, E.421, F.422 Ligands: GOL.18 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:A.53, B:W.56, B:W.56, B:L.83, B:F.104, B:E.421 Salt bridges: B:D.46 USS.19: 15 residues within 4Å: Chain C: W.33, D.46, I.48, A.53, W.56, R.57, V.60, L.83, M.85, S.103, F.104, E.223, E.421, F.422 Ligands: GOL.27 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:A.53, C:W.56, C:W.56, C:L.83, C:F.104, C:E.421 Salt bridges: C:D.46 USS.28: 15 residues within 4Å: Chain D: W.33, D.46, I.48, A.53, W.56, R.57, V.60, L.83, M.85, S.103, F.104, E.223, E.421, F.422 Ligands: GOL.36 7 PLIP interactions: 7 interactions with chain D Hydrophobic interactions: D:A.53, D:W.56, D:W.56, D:L.83, D:F.104, D:E.421 Salt bridges: D:D.46 USS.37: 15 residues within 4Å: Chain E: W.33, D.46, I.48, A.53, W.56, R.57, V.60, L.83, M.85, S.103, F.104, E.223, E.421, F.422 Ligands: GOL.45 7 PLIP interactions: 7 interactions with chain E Hydrophobic interactions: E:A.53, E:W.56, E:W.56, E:L.83, E:F.104, E:E.421 Salt bridges: E:D.46 USS.46: 15 residues within 4Å: Chain F: W.33, D.46, I.48, A.53, W.56, R.57, V.60, L.83, M.85, S.103, F.104, E.223, E.421, F.422 Ligands: GOL.54 7 PLIP interactions: 7 interactions with chain F Hydrophobic interactions: F:A.53, F:W.56, F:W.56, F:L.83, F:F.104, F:E.421 Salt bridges: F:D.46

30 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 5 residues within 4Å: Chain A: H.125, R.126, A.129, R.317, M.319 Ligand excluded by PLIP GOL.3: 6 residues within 4Å: Chain A: L.157, S.259, R.262, I.288, T.418, A.419 Ligand excluded by PLIP GOL.6: 6 residues within 4Å: Chain A: W.33, R.57, V.60, P.61, T.62, A.65 Ligand excluded by PLIP GOL.8: 8 residues within 4Å: Chain A: F.44, S.103, F.104, V.105, H.139, S.141, Y.146 Ligands: GOL.9 Ligand excluded by PLIP GOL.9: 7 residues within 4Å: Chain A: F.44, D.46, S.103, F.104, F.422 Ligands: USS.1, GOL.8 Ligand excluded by PLIP GOL.11: 5 residues within 4Å: Chain B: H.125, R.126, A.129, R.317, M.319 Ligand excluded by PLIP GOL.12: 6 residues within 4Å: Chain B: L.157, S.259, R.262, I.288, T.418, A.419 Ligand excluded by PLIP GOL.15: 6 residues within 4Å: Chain B: W.33, R.57, V.60, P.61, T.62, A.65 Ligand excluded by PLIP GOL.17: 8 residues within 4Å: Chain B: F.44, S.103, F.104, V.105, H.139, S.141, Y.146 Ligands: GOL.18 Ligand excluded by PLIP GOL.18: 7 residues within 4Å: Chain B: F.44, D.46, S.103, F.104, F.422 Ligands: USS.10, GOL.17 Ligand excluded by PLIP GOL.20: 5 residues within 4Å: Chain C: H.125, R.126, A.129, R.317, M.319 Ligand excluded by PLIP GOL.21: 6 residues within 4Å: Chain C: L.157, S.259, R.262, I.288, T.418, A.419 Ligand excluded by PLIP GOL.24: 6 residues within 4Å: Chain C: W.33, R.57, V.60, P.61, T.62, A.65 Ligand excluded by PLIP GOL.26: 8 residues within 4Å: Chain C: F.44, S.103, F.104, V.105, H.139, S.141, Y.146 Ligands: GOL.27 Ligand excluded by PLIP GOL.27: 7 residues within 4Å: Chain C: F.44, D.46, S.103, F.104, F.422 Ligands: USS.19, GOL.26 Ligand excluded by PLIP GOL.29: 5 residues within 4Å: Chain D: H.125, R.126, A.129, R.317, M.319 Ligand excluded by PLIP GOL.30: 6 residues within 4Å: Chain D: L.157, S.259, R.262, I.288, T.418, A.419 Ligand excluded by PLIP GOL.33: 6 residues within 4Å: Chain D: W.33, R.57, V.60, P.61, T.62, A.65 Ligand excluded by PLIP GOL.35: 8 residues within 4Å: Chain D: F.44, S.103, F.104, V.105, H.139, S.141, Y.146 Ligands: GOL.36 Ligand excluded by PLIP GOL.36: 7 residues within 4Å: Chain D: F.44, D.46, S.103, F.104, F.422 Ligands: USS.28, GOL.35 Ligand excluded by PLIP GOL.38: 5 residues within 4Å: Chain E: H.125, R.126, A.129, R.317, M.319 Ligand excluded by PLIP GOL.39: 6 residues within 4Å: Chain E: L.157, S.259, R.262, I.288, T.418, A.419 Ligand excluded by PLIP GOL.42: 6 residues within 4Å: Chain E: W.33, R.57, V.60, P.61, T.62, A.65 Ligand excluded by PLIP GOL.44: 8 residues within 4Å: Chain E: F.44, S.103, F.104, V.105, H.139, S.141, Y.146 Ligands: GOL.45 Ligand excluded by PLIP GOL.45: 7 residues within 4Å: Chain E: F.44, D.46, S.103, F.104, F.422 Ligands: USS.37, GOL.44 Ligand excluded by PLIP GOL.47: 5 residues within 4Å: Chain F: H.125, R.126, A.129, R.317, M.319 Ligand excluded by PLIP GOL.48: 6 residues within 4Å: Chain F: L.157, S.259, R.262, I.288, T.418, A.419 Ligand excluded by PLIP GOL.51: 6 residues within 4Å: Chain F: W.33, R.57, V.60, P.61, T.62, A.65 Ligand excluded by PLIP GOL.53: 8 residues within 4Å: Chain F: F.44, S.103, F.104, V.105, H.139, S.141, Y.146 Ligands: GOL.54 Ligand excluded by PLIP GOL.54: 7 residues within 4Å: Chain F: F.44, D.46, S.103, F.104, F.422 Ligands: USS.46, GOL.53 Ligand excluded by PLIP

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

DMS.4: 3 residues within 4Å: Chain A: E.159, R.257, W.309 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.257 Salt bridges: A:E.159 pi-Cation interactions: A:W.309, A:W.309 DMS.5: 7 residues within 4Å: Chain A: A.367, E.368, I.369, E.370, R.396, T.397, K.398 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.398 Salt bridges: A:E.370 DMS.13: 3 residues within 4Å: Chain B: E.159, R.257, W.309 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.257 Salt bridges: B:E.159 pi-Cation interactions: B:W.309, B:W.309 DMS.14: 7 residues within 4Å: Chain B: A.367, E.368, I.369, E.370, R.396, T.397, K.398 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.398 Salt bridges: B:E.370 DMS.22: 3 residues within 4Å: Chain C: E.159, R.257, W.309 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:R.257 Salt bridges: C:E.159 pi-Cation interactions: C:W.309, C:W.309 DMS.23: 7 residues within 4Å: Chain C: A.367, E.368, I.369, E.370, R.396, T.397, K.398 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:K.398 Salt bridges: C:E.370 DMS.31: 3 residues within 4Å: Chain D: E.159, R.257, W.309 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:R.257 Salt bridges: D:E.159 pi-Cation interactions: D:W.309, D:W.309 DMS.32: 7 residues within 4Å: Chain D: A.367, E.368, I.369, E.370, R.396, T.397, K.398 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:K.398 Salt bridges: D:E.370 DMS.40: 3 residues within 4Å: Chain E: E.159, R.257, W.309 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:R.257 Salt bridges: E:E.159 pi-Cation interactions: E:W.309, E:W.309 DMS.41: 7 residues within 4Å: Chain E: A.367, E.368, I.369, E.370, R.396, T.397, K.398 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:K.398 Salt bridges: E:E.370 DMS.49: 3 residues within 4Å: Chain F: E.159, R.257, W.309 4 PLIP interactions: 4 interactions with chain F Hydrogen bonds: F:R.257 Salt bridges: F:E.159 pi-Cation interactions: F:W.309, F:W.309 DMS.50: 7 residues within 4Å: Chain F: A.367, E.368, I.369, E.370, R.396, T.397, K.398 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:K.398 Salt bridges: F:E.370

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

PEG.7: 8 residues within 4Å: Chain A: L.261, H.269, I.287, T.289, H.290, D.293, P.294, Q.417 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.289, A:T.289 PEG.16: 8 residues within 4Å: Chain B: L.261, H.269, I.287, T.289, H.290, D.293, P.294, Q.417 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.289, B:T.289 PEG.25: 8 residues within 4Å: Chain C: L.261, H.269, I.287, T.289, H.290, D.293, P.294, Q.417 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:T.289, C:T.289 PEG.34: 8 residues within 4Å: Chain D: L.261, H.269, I.287, T.289, H.290, D.293, P.294, Q.417 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:T.289 PEG.43: 8 residues within 4Å: Chain E: L.261, H.269, I.287, T.289, H.290, D.293, P.294, Q.417 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:T.289 PEG.52: 8 residues within 4Å: Chain F: L.261, H.269, I.287, T.289, H.290, D.293, P.294, Q.417 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:T.289

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Punetha, A. et al., Structure-based design of haloperidol analogues as inhibitors of acetyltransferase Eis from Mycobacterium tuberculosis to overcome kanamycin resistance. Rsc Med Chem (2021)

Release Date

2021-06-02

Peptides

N-acetyltransferase Eis: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
AAA

B
AAA

C
AAA

D
AAA

E
AAA

F
AAA

N-acetyltransferase Eis

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