SMTL ID : 9mva.1 (1 other biounit)

Mycobacterium abscessus Eis2 in complex with Non-hydrolyzable CoenzymeA

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-hexamer

Ligands

6 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.1: 5 residues within 4Å: Chain A: F.27, F.118, A.119, S.120 Ligands: SOP.2 No protein-ligand interaction detected (PLIP) EDO.9: 4 residues within 4Å: Chain B: F.27, A.119, S.120 Ligands: SOP.10 1 PLIP interactions: 1 interactions with chain B Water bridges: B:A.119 EDO.19: 4 residues within 4Å: Chain C: F.27, S.120 Ligands: SOP.20, PGE.25 No protein-ligand interaction detected (PLIP) EDO.29: 5 residues within 4Å: Chain D: F.27, F.118, A.119, S.120 Ligands: SOP.30 No protein-ligand interaction detected (PLIP) EDO.37: 4 residues within 4Å: Chain E: F.27, A.119, S.120 Ligands: SOP.38 1 PLIP interactions: 1 interactions with chain E Water bridges: E:A.119 EDO.47: 4 residues within 4Å: Chain F: F.27, S.120 Ligands: SOP.48, PGE.53 No protein-ligand interaction detected (PLIP)

6 x SOP: [(2R,3S,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-4-HYDROXY-3-(PHOSPHONOOXY)TETRAHYDROFURAN-2-YL]METHYL (3R)-3-HYDROXY-2,2-DIMETHYL-4-OXO-4-{[3-OXO-3-({2-[(2-OXOPROPYL)THIO]ETHYL}AMINO)PROPYL]AMINO}BUTYL DIHYDROGEN DIPHOSPHATE(Non-covalent)

SOP.2: 26 residues within 4Å: Chain A: V.26, F.27, V.81, T.82, A.83, V.84, T.85, V.86, R.91, R.92, R.93, G.94, L.95, L.96, T.97, F.118, A.119, S.120, E.121, L.123, I.124, Y.125, R.127 Chain B: D.267, L.268 Ligands: EDO.1 30 PLIP interactions: 29 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:V.26, A:F.27, A:V.81, A:V.84, A:V.84, A:I.124 Hydrogen bonds: A:V.84, A:V.84, A:V.86, A:R.92, A:R.92, A:R.92, A:R.92, A:G.94, A:L.95, A:L.96, A:T.97, A:T.97, A:S.120, A:E.121, B:D.267 Water bridges: A:R.93, A:R.93, A:E.121, A:R.127, A:R.127, A:R.127, A:R.127 Salt bridges: A:R.92 pi-Cation interactions: A:R.92 SOP.10: 26 residues within 4Å: Chain B: V.26, F.27, V.81, T.82, A.83, V.84, T.85, V.86, R.91, R.92, R.93, G.94, L.95, L.96, T.97, F.118, A.119, S.120, E.121, L.123, I.124, Y.125, R.127 Chain C: D.267, L.268 Ligands: EDO.9 31 PLIP interactions: 30 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: B:V.26, B:F.27, B:V.81, B:V.84, B:V.86, B:I.124 Hydrogen bonds: B:V.84, B:V.84, B:V.86, B:R.92, B:R.92, B:R.92, B:R.92, B:G.94, B:L.95, B:L.96, B:T.97, B:T.97, B:S.120, B:E.121, C:D.267 Water bridges: B:A.83, B:R.93, B:R.93, B:E.121, B:R.127, B:R.127, B:R.127, B:R.127 Salt bridges: B:R.92 pi-Cation interactions: B:R.92 SOP.20: 26 residues within 4Å: Chain A: D.267, L.268 Chain C: V.26, F.27, V.81, T.82, A.83, V.84, T.85, V.86, R.91, R.92, R.93, G.94, L.95, L.96, T.97, F.118, A.119, S.120, E.121, L.123, I.124, Y.125, R.127 Ligands: EDO.19 31 PLIP interactions: 30 interactions with chain C, 1 interactions with chain A Hydrophobic interactions: C:V.26, C:F.27, C:V.84, C:V.86, C:I.124 Hydrogen bonds: C:A.83, C:V.84, C:V.84, C:V.86, C:R.92, C:R.92, C:R.92, C:R.92, C:G.94, C:L.95, C:L.96, C:T.97, C:T.97, C:S.120, C:E.121, A:D.267 Water bridges: C:R.91, C:R.93, C:R.93, C:E.121, C:R.127, C:R.127, C:R.127, C:R.127 Salt bridges: C:R.92 pi-Cation interactions: C:R.92 SOP.30: 26 residues within 4Å: Chain D: V.26, F.27, V.81, T.82, A.83, V.84, T.85, V.86, R.91, R.92, R.93, G.94, L.95, L.96, T.97, F.118, A.119, S.120, E.121, L.123, I.124, Y.125, R.127 Chain E: D.267, L.268 Ligands: EDO.29 29 PLIP interactions: 29 interactions with chain D Hydrophobic interactions: D:V.26, D:F.27, D:V.81, D:V.84, D:V.84, D:I.124 Hydrogen bonds: D:V.84, D:V.84, D:V.86, D:R.92, D:R.92, D:R.92, D:R.92, D:G.94, D:L.95, D:L.96, D:T.97, D:T.97, D:T.97, D:S.120, D:E.121 Water bridges: D:R.93, D:R.93, D:R.127, D:R.127, D:R.127, D:R.127 Salt bridges: D:R.92 pi-Cation interactions: D:R.92 SOP.38: 26 residues within 4Å: Chain E: V.26, F.27, V.81, T.82, A.83, V.84, T.85, V.86, R.91, R.92, R.93, G.94, L.95, L.96, T.97, F.118, A.119, S.120, E.121, L.123, I.124, Y.125, R.127 Chain F: D.267, L.268 Ligands: EDO.37 30 PLIP interactions: 30 interactions with chain E Hydrophobic interactions: E:V.26, E:F.27, E:V.81, E:V.84, E:V.86, E:I.124 Hydrogen bonds: E:V.84, E:V.84, E:V.86, E:R.92, E:R.92, E:R.92, E:R.92, E:G.94, E:L.95, E:L.96, E:T.97, E:T.97, E:T.97, E:S.120, E:E.121 Water bridges: E:A.83, E:R.93, E:R.93, E:R.127, E:R.127, E:R.127, E:R.127 Salt bridges: E:R.92 pi-Cation interactions: E:R.92 SOP.48: 26 residues within 4Å: Chain D: D.267, L.268 Chain F: V.26, F.27, V.81, T.82, A.83, V.84, T.85, V.86, R.91, R.92, R.93, G.94, L.95, L.96, T.97, F.118, A.119, S.120, E.121, L.123, I.124, Y.125, R.127 Ligands: EDO.47 30 PLIP interactions: 30 interactions with chain F Hydrophobic interactions: F:V.26, F:F.27, F:V.84, F:V.86, F:I.124 Hydrogen bonds: F:A.83, F:V.84, F:V.84, F:V.86, F:R.92, F:R.92, F:R.92, F:R.92, F:G.94, F:L.95, F:L.96, F:T.97, F:T.97, F:T.97, F:S.120, F:E.121 Water bridges: F:R.91, F:R.93, F:R.93, F:R.127, F:R.127, F:R.127, F:R.127 Salt bridges: F:R.92 pi-Cation interactions: F:R.92

10 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.3: 7 residues within 4Å: Chain A: T.328, A.360, L.361, T.362, G.383, L.384, T.386 1 PLIP interactions: 1 interactions with chain A Water bridges: A:T.328 PGE.11: 6 residues within 4Å: Chain B: T.328, A.360, L.361, G.383, L.384, T.386 1 PLIP interactions: 1 interactions with chain B Water bridges: B:L.361 PGE.22: 7 residues within 4Å: Chain C: T.328, A.360, L.361, T.362, G.383, L.384, T.386 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:T.328 PGE.23: 3 residues within 4Å: Chain C: R.108, S.109, D.307 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:S.109 PGE.25: 8 residues within 4Å: Chain A: W.234 Chain C: M.20, A.23, Y.24, F.27, R.29, A.83 Ligands: EDO.19 5 PLIP interactions: 1 interactions with chain A, 4 interactions with chain C Water bridges: A:W.234, C:R.29, C:N.39, C:N.39 Hydrogen bonds: C:R.29 PGE.31: 7 residues within 4Å: Chain D: T.328, A.360, L.361, T.362, G.383, L.384, T.386 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:T.386 Water bridges: D:T.328 PGE.39: 6 residues within 4Å: Chain E: T.328, A.360, L.361, G.383, L.384, T.386 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:T.386 Water bridges: E:T.328 PGE.50: 7 residues within 4Å: Chain F: T.328, A.360, L.361, T.362, G.383, L.384, T.386 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:T.386 Water bridges: F:T.328 PGE.51: 3 residues within 4Å: Chain F: R.108, S.109, D.307 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:S.109 PGE.53: 8 residues within 4Å: Chain D: W.234 Chain F: M.20, A.23, Y.24, F.27, R.29, A.83 Ligands: EDO.47 5 PLIP interactions: 1 interactions with chain D, 4 interactions with chain F Water bridges: D:W.234, F:Y.24, F:R.29, F:N.39 Hydrogen bonds: F:R.29

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

PEG.4: 9 residues within 4Å: Chain A: G.372, G.373, V.374, S.375, A.397, G.401 Chain D: Q.280, W.402, P.403 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain A Hydrogen bonds: D:Q.280, D:W.402 Water bridges: A:G.373 PEG.5: 4 residues within 4Å: Chain A: M.20, Y.24, F.27, R.29 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.29 PEG.12: 5 residues within 4Å: Chain B: G.72, G.73, P.180, W.402 Chain F: Q.394 1 PLIP interactions: 1 interactions with chain B Water bridges: B:G.72 PEG.13: 9 residues within 4Å: Chain B: G.372, G.373, V.374, S.375, A.397, G.401 Chain F: Q.280, W.402, P.403 4 PLIP interactions: 2 interactions with chain F, 2 interactions with chain B Hydrogen bonds: F:Q.280 Water bridges: F:W.402, B:G.373, B:T.398 PEG.14: 4 residues within 4Å: Chain B: Y.24, F.27, R.29, A.83 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:A.83 Water bridges: B:T.82 PEG.21: 4 residues within 4Å: Chain C: G.72, G.73, A.74, R.316 2 PLIP interactions: 2 interactions with chain C Water bridges: C:G.73, C:R.316 PEG.24: 10 residues within 4Å: Chain C: G.372, G.373, V.374, S.375, A.397, T.398, G.401 Chain E: Q.280, W.402, P.403 4 PLIP interactions: 2 interactions with chain E, 2 interactions with chain C Hydrogen bonds: E:Q.280, E:W.402, C:G.373 Water bridges: C:L.376 PEG.32: 9 residues within 4Å: Chain A: Q.280, W.402, P.403 Chain D: G.372, G.373, V.374, S.375, A.397, G.401 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain D Hydrogen bonds: A:Q.280, A:W.402 Water bridges: D:G.373 PEG.33: 4 residues within 4Å: Chain D: M.20, Y.24, F.27, R.29 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:R.29 PEG.40: 5 residues within 4Å: Chain C: Q.394 Chain E: G.72, G.73, P.180, W.402 1 PLIP interactions: 1 interactions with chain E Water bridges: E:G.72 PEG.41: 9 residues within 4Å: Chain C: Q.280, W.402, P.403 Chain E: G.372, G.373, V.374, S.375, A.397, G.401 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain E Hydrogen bonds: C:Q.280 Water bridges: C:W.402, E:G.373, E:T.398 PEG.42: 4 residues within 4Å: Chain E: Y.24, F.27, R.29, A.83 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:A.83 Water bridges: E:T.82 PEG.49: 4 residues within 4Å: Chain F: G.72, G.73, A.74, R.316 2 PLIP interactions: 2 interactions with chain F Water bridges: F:G.73, F:R.316 PEG.52: 10 residues within 4Å: Chain B: Q.280, W.402, P.403 Chain F: G.372, G.373, V.374, S.375, A.397, T.398, G.401 4 PLIP interactions: 2 interactions with chain F, 2 interactions with chain B Hydrogen bonds: F:G.373, B:Q.280, B:W.402 Water bridges: F:L.376

6 x CL: CHLORIDE ION(Non-functional Binders)

CL.6: 4 residues within 4Å: Chain A: G.129, T.362, V.363, R.364 Ligand excluded by PLIP CL.15: 4 residues within 4Å: Chain B: G.129, T.362, V.363, R.364 Ligand excluded by PLIP CL.26: 4 residues within 4Å: Chain C: D.330, T.362, V.363, R.364 Ligand excluded by PLIP CL.34: 4 residues within 4Å: Chain D: G.129, T.362, V.363, R.364 Ligand excluded by PLIP CL.43: 4 residues within 4Å: Chain E: G.129, T.362, V.363, R.364 Ligand excluded by PLIP CL.54: 4 residues within 4Å: Chain F: D.330, T.362, V.363, R.364 Ligand excluded by PLIP

14 x NA: SODIUM ION(Non-functional Binders)

NA.7: 1 residues within 4Å: Chain A: G.276 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.276 NA.8: 0 residues within 4Å: (No contacts) 1 PLIP interactions: 1 interactions with chain A Water bridges: A:T.251 NA.16: 5 residues within 4Å: Chain B: E.121 Chain C: R.144, D.267, L.268, R.270 6 PLIP interactions: 1 interactions with chain B, 5 interactions with chain C Hydrogen bonds: B:E.121, C:R.144, C:L.268, C:R.270, C:R.270 Water bridges: C:R.144 NA.17: 0 residues within 4Å: (No contacts) 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain F Water bridges: B:G.181, F:S.381 NA.18: 2 residues within 4Å: Chain B: G.276, A.408 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:A.408 NA.27: 1 residues within 4Å: Chain C: G.276 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:G.276 NA.28: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) NA.35: 1 residues within 4Å: Chain D: G.276 5 PLIP interactions: 5 interactions with chain D Water bridges: D:Y.274, D:Y.274, D:G.276, D:A.408, D:P.409 NA.36: 0 residues within 4Å: (No contacts) 2 PLIP interactions: 2 interactions with chain D Water bridges: D:G.250, D:T.251 NA.44: 5 residues within 4Å: Chain E: E.121 Chain F: R.144, D.267, L.268, R.270 7 PLIP interactions: 6 interactions with chain F, 1 interactions with chain E Hydrogen bonds: F:R.144, F:L.268, F:R.270, F:R.270, E:E.121 Water bridges: F:R.144, F:D.267 NA.45: 0 residues within 4Å: (No contacts) 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain E Water bridges: C:S.381, E:G.181 NA.46: 2 residues within 4Å: Chain E: G.276, A.408 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:G.276 Water bridges: E:E.247, E:Y.274 NA.55: 1 residues within 4Å: Chain F: G.276 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:G.276 Water bridges: F:E.247 NA.56: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jayasinghe, T.D. et al., Mycobacterium abscessus Eis2 in complex with Non-hydrolyzable CoenzymeA. To Be Published

Release Date

2025-01-29

Peptides

Amikacin resistance N-acetyltransferase Eis2: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
D

C
E

D
A

E
D

F
E

Amikacin resistance N-acetyltransferase Eis2

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