SMTL ID : 9mva.2 (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

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

EDO.1: 4 residues within 4Å: Chain A: F.27, F.118, S.120 Ligands: SOP.2 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.120 EDO.12: 4 residues within 4Å: Chain B: F.27, A.119, S.120 Ligands: SOP.13 No protein-ligand interaction detected (PLIP) EDO.14: 2 residues within 4Å: Chain B: R.108, G.111 No protein-ligand interaction detected (PLIP) EDO.21: 4 residues within 4Å: Chain C: F.27, A.119, S.120 Ligands: SOP.22 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:A.119, C:S.120 EDO.32: 4 residues within 4Å: Chain D: F.27, F.118, S.120 Ligands: SOP.33 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:S.120 EDO.43: 4 residues within 4Å: Chain E: F.27, A.119, S.120 Ligands: SOP.44 No protein-ligand interaction detected (PLIP) EDO.45: 2 residues within 4Å: Chain E: R.108, G.111 No protein-ligand interaction detected (PLIP) EDO.52: 4 residues within 4Å: Chain F: F.27, A.119, S.120 Ligands: SOP.53 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:A.119, F:S.120

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 28 PLIP interactions: 28 interactions with chain A Hydrophobic interactions: A:V.26, A:F.27, 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:T.97, A:S.120, A:E.121 Water bridges: A:R.93, A:R.93, A:R.127, A:R.127, A:R.127, A:R.127 Salt bridges: A:R.92 pi-Cation interactions: A:R.92 SOP.13: 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.12 29 PLIP interactions: 29 interactions with chain B Hydrophobic interactions: B:V.26, B:F.27, B:V.81, B:V.84, B:I.124 Hydrogen bonds: B:A.83, 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:T.97, B:S.120, B:E.121 Water bridges: B:R.93, B:R.93, B:R.127, B:R.127, B:R.127, B:R.127 Salt bridges: B:R.92 pi-Cation interactions: B:R.92 SOP.22: 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.21 29 PLIP interactions: 29 interactions with chain C Hydrophobic interactions: C:V.26, C:F.27, C:V.84, C:V.86, C:I.124 Hydrogen bonds: 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:T.97, C:S.120, C:E.121 Water bridges: C:A.83, C:R.93, C:R.93, C:R.127, C:R.127, C:R.127, C:R.127 Salt bridges: C:R.92 pi-Cation interactions: C:R.92 SOP.33: 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.32 29 PLIP interactions: 28 interactions with chain D, 1 interactions with chain E Hydrophobic interactions: D:V.26, D:F.27, 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:S.120, D:E.121, E:D.267 Water bridges: D:R.93, D:R.93, D:E.121, D:R.127, D:R.127, D:R.127, D:R.127 Salt bridges: D:R.92 pi-Cation interactions: D:R.92 SOP.44: 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.43 30 PLIP interactions: 29 interactions with chain E, 1 interactions with chain F Hydrophobic interactions: E:V.26, E:F.27, E:V.81, E:V.84, E:I.124 Hydrogen bonds: E:A.83, 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:S.120, E:E.121, F:D.267 Water bridges: E:R.93, E:R.93, E:E.121, E:R.127, E:R.127, E:R.127, E:R.127 Salt bridges: E:R.92 pi-Cation interactions: E:R.92 SOP.53: 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.52 30 PLIP interactions: 29 interactions with chain F, 1 interactions with chain D Hydrophobic interactions: F:V.26, F:F.27, F:V.84, F:V.86, F:I.124 Hydrogen bonds: 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:S.120, F:E.121, D:D.267 Water bridges: F:A.83, F:R.93, F:R.93, F:E.121, F:R.127, F:R.127, F:R.127, F:R.127 Salt bridges: F:R.92 pi-Cation interactions: F:R.92

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

PEG.3: 3 residues within 4Å: Chain A: R.108, S.109, D.307 Ligand excluded by PLIP PEG.5: 5 residues within 4Å: Chain A: G.72, G.73, P.180, W.402 Chain D: Q.394 Ligand excluded by PLIP PEG.6: 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 Ligand excluded by PLIP PEG.7: 5 residues within 4Å: Chain A: M.20, A.23, Y.24, F.27, R.29 Ligand excluded by PLIP PEG.16: 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 Ligand excluded by PLIP PEG.17: 5 residues within 4Å: Chain B: M.20, Y.24, F.27, R.29, A.83 Ligand excluded by PLIP PEG.24: 4 residues within 4Å: Chain C: G.72, G.73, A.74, R.316 Ligand excluded by PLIP PEG.25: 2 residues within 4Å: Chain C: R.108, D.307 Ligand excluded by PLIP PEG.26: 9 residues within 4Å: Chain C: G.372, G.373, V.374, S.375, A.397, G.401 Chain E: Q.280, W.402, P.403 Ligand excluded by PLIP PEG.28: 2 residues within 4Å: Chain C: K.41, E.44 Ligand excluded by PLIP PEG.34: 3 residues within 4Å: Chain D: R.108, S.109, D.307 Ligand excluded by PLIP PEG.36: 5 residues within 4Å: Chain A: Q.394 Chain D: G.72, G.73, P.180, W.402 Ligand excluded by PLIP PEG.37: 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 Ligand excluded by PLIP PEG.38: 5 residues within 4Å: Chain D: M.20, A.23, Y.24, F.27, R.29 Ligand excluded by PLIP PEG.47: 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 Ligand excluded by PLIP PEG.48: 5 residues within 4Å: Chain E: M.20, Y.24, F.27, R.29, A.83 Ligand excluded by PLIP PEG.55: 4 residues within 4Å: Chain F: G.72, G.73, A.74, R.316 Ligand excluded by PLIP PEG.56: 2 residues within 4Å: Chain F: R.108, D.307 Ligand excluded by PLIP PEG.57: 9 residues within 4Å: Chain B: Q.280, W.402, P.403 Chain F: G.372, G.373, V.374, S.375, A.397, G.401 Ligand excluded by PLIP PEG.59: 2 residues within 4Å: Chain F: K.41, E.44 Ligand excluded by PLIP

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

PGE.4: 5 residues within 4Å: Chain A: T.328, A.360, G.383, L.384, T.386 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.386 Water bridges: A:T.328 PGE.15: 7 residues within 4Å: Chain B: T.328, A.360, L.361, G.383, L.384, T.386 Chain F: T.151 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.386 Water bridges: B:L.361 PGE.23: 7 residues within 4Å: Chain C: T.328, A.360, L.361, G.383, L.384, T.386 Chain E: T.151 4 PLIP interactions: 2 interactions with chain E, 2 interactions with chain C Hydrogen bonds: E:T.151, C:T.328, C:T.386 Water bridges: E:D.153 PGE.27: 7 residues within 4Å: Chain A: W.234 Chain C: M.20, A.23, Y.24, F.27, R.29, A.83 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:R.29 Water bridges: C:N.39 PGE.35: 5 residues within 4Å: Chain D: T.328, A.360, G.383, L.384, T.386 1 PLIP interactions: 1 interactions with chain D Water bridges: D:L.361 PGE.46: 7 residues within 4Å: Chain C: T.151 Chain E: T.328, A.360, L.361, G.383, L.384, T.386 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:T.328 Water bridges: E:L.361, E:T.386 PGE.54: 7 residues within 4Å: Chain B: T.151 Chain F: T.328, A.360, L.361, G.383, L.384, T.386 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain F Hydrogen bonds: B:T.151, F:T.328, F:T.328 Water bridges: B:D.153 PGE.58: 7 residues within 4Å: Chain D: W.234 Chain F: M.20, A.23, Y.24, F.27, R.29, A.83 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:R.29 Water bridges: F:N.39

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

CL.8: 3 residues within 4Å: Chain A: T.362, V.363, R.364 Ligand excluded by PLIP CL.18: 4 residues within 4Å: Chain B: G.129, T.362, V.363, R.364 Ligand excluded by PLIP CL.29: 4 residues within 4Å: Chain C: D.330, T.362, V.363, R.364 Ligand excluded by PLIP CL.39: 3 residues within 4Å: Chain D: T.362, V.363, R.364 Ligand excluded by PLIP CL.49: 4 residues within 4Å: Chain E: G.129, T.362, V.363, R.364 Ligand excluded by PLIP CL.60: 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.9: 5 residues within 4Å: Chain A: E.121 Chain B: R.144, D.267, L.268, R.270 7 PLIP interactions: 6 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:R.144, B:L.268, B:R.270, B:R.270, A:E.121 Water bridges: B:R.144, B:D.267 NA.10: 1 residues within 4Å: Chain A: G.276 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.276 Water bridges: A:E.247 NA.11: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) NA.19: 0 residues within 4Å: (No contacts) 1 PLIP interactions: 1 interactions with chain B Water bridges: B:G.181 NA.20: 1 residues within 4Å: Chain B: G.276 3 PLIP interactions: 3 interactions with chain B Water bridges: B:Q.246, B:G.276, B:P.409 NA.30: 1 residues within 4Å: Chain C: G.276 1 PLIP interactions: 1 interactions with chain C Water bridges: C:P.409 NA.31: 0 residues within 4Å: (No contacts) 1 PLIP interactions: 1 interactions with chain C Water bridges: C:G.181 NA.40: 5 residues within 4Å: Chain D: E.121 Chain E: R.144, D.267, L.268, R.270 7 PLIP interactions: 7 interactions with chain E Hydrogen bonds: E:R.144, E:L.268, E:R.270, E:R.270 Water bridges: E:R.144, E:R.144, E:V.269 NA.41: 1 residues within 4Å: Chain D: G.276 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:A.408 NA.42: 0 residues within 4Å: (No contacts) 1 PLIP interactions: 1 interactions with chain D Water bridges: D:T.251 NA.50: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) NA.51: 1 residues within 4Å: Chain E: G.276 2 PLIP interactions: 2 interactions with chain E Water bridges: E:E.247, E:P.409 NA.61: 1 residues within 4Å: Chain F: G.276 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:A.408 NA.62: 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
B

B
C

C
F

D
B

E
C

F
F

Amikacin resistance N-acetyltransferase Eis2

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