SMTL ID : 6p3t.1

Crystal structure of Eis from Mycobacterium tuberculosis in complex with inhibitor SGT449

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-hexamer

Ligands

6 x NRS: N-methyl-N-(naphthalen-2-yl)-2,3-dioxo-1,2,3,4-tetrahydroquinoxaline-6-sulfonamide(Non-covalent)

NRS.1: 14 residues within 4Å: Chain A: F.44, D.46, F.47, I.48, A.53, W.56, R.57, V.60, L.83, M.85, S.103, F.104, S.141, F.422 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:F.44, 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:D.46, A:I.48 pi-Stacking: A:F.44, A:F.44 NRS.13: 14 residues within 4Å: Chain B: F.44, D.46, F.47, I.48, A.53, W.56, R.57, V.60, L.83, M.85, S.103, F.104, S.141, F.422 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:F.44, 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:D.46, B:I.48 pi-Stacking: B:F.44, B:F.44 NRS.25: 14 residues within 4Å: Chain C: F.44, D.46, F.47, I.48, A.53, W.56, R.57, V.60, L.83, M.85, S.103, F.104, S.141, F.422 14 PLIP interactions: 14 interactions with chain C Hydrophobic interactions: C:F.44, 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:D.46, C:I.48 pi-Stacking: C:F.44, C:F.44 NRS.37: 14 residues within 4Å: Chain D: F.44, D.46, F.47, I.48, A.53, W.56, R.57, V.60, L.83, M.85, S.103, F.104, S.141, F.422 14 PLIP interactions: 14 interactions with chain D Hydrophobic interactions: D:F.44, 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:D.46, D:I.48 pi-Stacking: D:F.44, D:F.44 NRS.49: 14 residues within 4Å: Chain E: F.44, D.46, F.47, I.48, A.53, W.56, R.57, V.60, L.83, M.85, S.103, F.104, S.141, F.422 14 PLIP interactions: 14 interactions with chain E Hydrophobic interactions: E:F.44, 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:D.46, E:I.48 pi-Stacking: E:F.44, E:F.44 NRS.61: 14 residues within 4Å: Chain F: F.44, D.46, F.47, I.48, A.53, W.56, R.57, V.60, L.83, M.85, S.103, F.104, S.141, F.422 14 PLIP interactions: 14 interactions with chain F Hydrophobic interactions: F:F.44, 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:D.46, F:I.48 pi-Stacking: F:F.44, F:F.44

18 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 7 residues within 4Å: Chain A: R.118, C.121, A.122, H.125, R.148, F.149, R.317 Ligand excluded by PLIP GOL.3: 5 residues within 4Å: Chain A: P.61, T.62, Y.84, S.131, Y.133 Ligand excluded by PLIP GOL.11: 9 residues within 4Å: Chain A: G.152, P.153, D.374, V.375, S.378, L.389, R.394 Chain E: H.297, T.302 Ligand excluded by PLIP GOL.14: 7 residues within 4Å: Chain B: R.118, C.121, A.122, H.125, R.148, F.149, R.317 Ligand excluded by PLIP GOL.15: 5 residues within 4Å: Chain B: P.61, T.62, Y.84, S.131, Y.133 Ligand excluded by PLIP GOL.23: 9 residues within 4Å: Chain B: G.152, P.153, D.374, V.375, S.378, L.389, R.394 Chain D: H.297, T.302 Ligand excluded by PLIP GOL.26: 7 residues within 4Å: Chain C: R.118, C.121, A.122, H.125, R.148, F.149, R.317 Ligand excluded by PLIP GOL.27: 5 residues within 4Å: Chain C: P.61, T.62, Y.84, S.131, Y.133 Ligand excluded by PLIP GOL.35: 9 residues within 4Å: Chain C: G.152, P.153, D.374, V.375, S.378, L.389, R.394 Chain F: H.297, T.302 Ligand excluded by PLIP GOL.38: 7 residues within 4Å: Chain D: R.118, C.121, A.122, H.125, R.148, F.149, R.317 Ligand excluded by PLIP GOL.39: 5 residues within 4Å: Chain D: P.61, T.62, Y.84, S.131, Y.133 Ligand excluded by PLIP GOL.47: 9 residues within 4Å: Chain B: H.297, T.302 Chain D: G.152, P.153, D.374, V.375, S.378, L.389, R.394 Ligand excluded by PLIP GOL.50: 7 residues within 4Å: Chain E: R.118, C.121, A.122, H.125, R.148, F.149, R.317 Ligand excluded by PLIP GOL.51: 5 residues within 4Å: Chain E: P.61, T.62, Y.84, S.131, Y.133 Ligand excluded by PLIP GOL.59: 9 residues within 4Å: Chain A: H.297, T.302 Chain E: G.152, P.153, D.374, V.375, S.378, L.389, R.394 Ligand excluded by PLIP GOL.62: 7 residues within 4Å: Chain F: R.118, C.121, A.122, H.125, R.148, F.149, R.317 Ligand excluded by PLIP GOL.63: 5 residues within 4Å: Chain F: P.61, T.62, Y.84, S.131, Y.133 Ligand excluded by PLIP GOL.71: 9 residues within 4Å: Chain C: H.297, T.302 Chain F: G.152, P.153, D.374, V.375, S.378, L.389, R.394 Ligand excluded by PLIP

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

PEG.4: 11 residues within 4Å: Chain A: E.260, L.261, R.262, H.269, I.287, I.288, T.289, H.290, D.293, Q.417 Ligands: SO4.6 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:L.261, A:R.262, A:T.289, A:Q.417 Water bridges: A:W.202, A:A.263 PEG.16: 11 residues within 4Å: Chain B: E.260, L.261, R.262, H.269, I.287, I.288, T.289, H.290, D.293, Q.417 Ligands: SO4.18 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:L.261, B:R.262, B:T.289, B:Q.417 Water bridges: B:W.202, B:A.263 PEG.28: 11 residues within 4Å: Chain C: E.260, L.261, R.262, H.269, I.287, I.288, T.289, H.290, D.293, Q.417 Ligands: SO4.30 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:L.261, C:R.262, C:T.289, C:Q.417 Water bridges: C:W.202, C:A.263 PEG.40: 11 residues within 4Å: Chain D: E.260, L.261, R.262, H.269, I.287, I.288, T.289, H.290, D.293, Q.417 Ligands: SO4.42 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:L.261, D:R.262, D:Q.417 Water bridges: D:W.202, D:A.263 PEG.52: 11 residues within 4Å: Chain E: E.260, L.261, R.262, H.269, I.287, I.288, T.289, H.290, D.293, Q.417 Ligands: SO4.54 5 PLIP interactions: 5 interactions with chain E Hydrogen bonds: E:L.261, E:R.262, E:Q.417 Water bridges: E:W.202, E:A.263 PEG.64: 11 residues within 4Å: Chain F: E.260, L.261, R.262, H.269, I.287, I.288, T.289, H.290, D.293, Q.417 Ligands: SO4.66 5 PLIP interactions: 5 interactions with chain F Hydrogen bonds: F:L.261, F:R.262, F:Q.417 Water bridges: F:W.202, F:A.263

18 x SO4: SULFATE ION(Non-functional Binders)

SO4.5: 10 residues within 4Å: Chain A: P.92, G.93, R.328, G.329, Y.330, A.331, A.411, S.412, D.413 Ligands: NH4.12 Ligand excluded by PLIP SO4.6: 7 residues within 4Å: Chain A: R.262, I.288, T.289, H.290, Q.417, T.418 Ligands: PEG.4 Ligand excluded by PLIP SO4.7: 3 residues within 4Å: Chain A: W.33, R.57, V.60 Ligand excluded by PLIP SO4.17: 10 residues within 4Å: Chain B: P.92, G.93, R.328, G.329, Y.330, A.331, A.411, S.412, D.413 Ligands: NH4.24 Ligand excluded by PLIP SO4.18: 7 residues within 4Å: Chain B: R.262, I.288, T.289, H.290, Q.417, T.418 Ligands: PEG.16 Ligand excluded by PLIP SO4.19: 3 residues within 4Å: Chain B: W.33, R.57, V.60 Ligand excluded by PLIP SO4.29: 10 residues within 4Å: Chain C: P.92, G.93, R.328, G.329, Y.330, A.331, A.411, S.412, D.413 Ligands: NH4.36 Ligand excluded by PLIP SO4.30: 7 residues within 4Å: Chain C: R.262, I.288, T.289, H.290, Q.417, T.418 Ligands: PEG.28 Ligand excluded by PLIP SO4.31: 3 residues within 4Å: Chain C: W.33, R.57, V.60 Ligand excluded by PLIP SO4.41: 10 residues within 4Å: Chain D: P.92, G.93, R.328, G.329, Y.330, A.331, A.411, S.412, D.413 Ligands: NH4.48 Ligand excluded by PLIP SO4.42: 7 residues within 4Å: Chain D: R.262, I.288, T.289, H.290, Q.417, T.418 Ligands: PEG.40 Ligand excluded by PLIP SO4.43: 3 residues within 4Å: Chain D: W.33, R.57, V.60 Ligand excluded by PLIP SO4.53: 10 residues within 4Å: Chain E: P.92, G.93, R.328, G.329, Y.330, A.331, A.411, S.412, D.413 Ligands: NH4.60 Ligand excluded by PLIP SO4.54: 7 residues within 4Å: Chain E: R.262, I.288, T.289, H.290, Q.417, T.418 Ligands: PEG.52 Ligand excluded by PLIP SO4.55: 3 residues within 4Å: Chain E: W.33, R.57, V.60 Ligand excluded by PLIP SO4.65: 10 residues within 4Å: Chain F: P.92, G.93, R.328, G.329, Y.330, A.331, A.411, S.412, D.413 Ligands: NH4.72 Ligand excluded by PLIP SO4.66: 7 residues within 4Å: Chain F: R.262, I.288, T.289, H.290, Q.417, T.418 Ligands: PEG.64 Ligand excluded by PLIP SO4.67: 3 residues within 4Å: Chain F: W.33, R.57, V.60 Ligand excluded by PLIP

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

DMS.8: 6 residues within 4Å: Chain A: A.367, E.368, I.369, E.370, T.397, K.398 Ligand excluded by PLIP DMS.9: 2 residues within 4Å: Chain A: T.418, E.421 Ligand excluded by PLIP DMS.10: 3 residues within 4Å: Chain A: H.125, R.317, M.319 Ligand excluded by PLIP DMS.20: 6 residues within 4Å: Chain B: A.367, E.368, I.369, E.370, T.397, K.398 Ligand excluded by PLIP DMS.21: 2 residues within 4Å: Chain B: T.418, E.421 Ligand excluded by PLIP DMS.22: 3 residues within 4Å: Chain B: H.125, R.317, M.319 Ligand excluded by PLIP DMS.32: 6 residues within 4Å: Chain C: A.367, E.368, I.369, E.370, T.397, K.398 Ligand excluded by PLIP DMS.33: 2 residues within 4Å: Chain C: T.418, E.421 Ligand excluded by PLIP DMS.34: 3 residues within 4Å: Chain C: H.125, R.317, M.319 Ligand excluded by PLIP DMS.44: 6 residues within 4Å: Chain D: A.367, E.368, I.369, E.370, T.397, K.398 Ligand excluded by PLIP DMS.45: 2 residues within 4Å: Chain D: T.418, E.421 Ligand excluded by PLIP DMS.46: 3 residues within 4Å: Chain D: H.125, R.317, M.319 Ligand excluded by PLIP DMS.56: 6 residues within 4Å: Chain E: A.367, E.368, I.369, E.370, T.397, K.398 Ligand excluded by PLIP DMS.57: 2 residues within 4Å: Chain E: T.418, E.421 Ligand excluded by PLIP DMS.58: 3 residues within 4Å: Chain E: H.125, R.317, M.319 Ligand excluded by PLIP DMS.68: 6 residues within 4Å: Chain F: A.367, E.368, I.369, E.370, T.397, K.398 Ligand excluded by PLIP DMS.69: 2 residues within 4Å: Chain F: T.418, E.421 Ligand excluded by PLIP DMS.70: 3 residues within 4Å: Chain F: H.125, R.317, M.319 Ligand excluded by PLIP

6 x NH4: AMMONIUM ION(Non-functional Binders)

NH4.12: 7 residues within 4Å: Chain A: P.92, G.93, P.207, S.412, D.413, V.414 Ligands: SO4.5 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.93, A:S.412 NH4.24: 7 residues within 4Å: Chain B: P.92, G.93, P.207, S.412, D.413, V.414 Ligands: SO4.17 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:G.93, B:S.412 NH4.36: 7 residues within 4Å: Chain C: P.92, G.93, P.207, S.412, D.413, V.414 Ligands: SO4.29 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:G.93, C:S.412 NH4.48: 7 residues within 4Å: Chain D: P.92, G.93, P.207, S.412, D.413, V.414 Ligands: SO4.41 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:G.93, D:D.413, D:D.413 NH4.60: 7 residues within 4Å: Chain E: P.92, G.93, P.207, S.412, D.413, V.414 Ligands: SO4.53 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:G.93, E:D.413, E:D.413 NH4.72: 7 residues within 4Å: Chain F: P.92, G.93, P.207, S.412, D.413, V.414 Ligands: SO4.65 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:G.93, F:D.413, F:D.413

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Green, K.D. et al., Probing the Robustness of Inhibitors of Tuberculosis Aminoglycoside Resistance Enzyme Eis by Mutagenesis. Acs Infect Dis. (2019)

Release Date

2019-09-04

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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