SMTL ID : 7b38.1

Torpedo californica acetylcholinesterase complexed with Mg+2

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

homo-dimer

Ligands

2 x NAG- FUC: alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-FUC.1: 3 residues within 4Å: Chain A: N.56, S.58, T.59 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.59, A:N.56, A:S.58 NAG-FUC.22: 3 residues within 4Å: Chain B: N.56, S.58, T.59 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.56, B:S.58

8 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 2 residues within 4Å: Chain A: D.323, D.389 6 PLIP interactions: 2 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:D.323, A:D.389, H2O.5, H2O.7, H2O.8, H2O.10 MG.19: 2 residues within 4Å: Chain A: E.136, H.468 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:E.136, A:H.468 MG.20: 2 residues within 4Å: Chain A: H.261, E.265 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:H.261, A:E.265 MG.21: 3 residues within 4Å: Chain A: H.468, E.481 Chain B: H.483 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Metal complexes: A:H.468, B:H.483, B:H.483 MG.23: 2 residues within 4Å: Chain B: D.323, D.389 6 PLIP interactions: 2 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:D.323, B:D.389, H2O.20, H2O.22, H2O.24, H2O.26 MG.40: 2 residues within 4Å: Chain B: E.136, H.468 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:E.136, B:H.468 MG.41: 2 residues within 4Å: Chain B: H.261, E.265 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:H.261, B:E.265 MG.42: 3 residues within 4Å: Chain A: H.483 Chain B: H.468, E.481 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Metal complexes: A:H.483, A:H.483, B:H.468

2 x ZN: ZINC ION(Non-covalent)

ZN.3: 2 residues within 4Å: Chain A: H.261, E.265 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.261, A:E.265, A:E.265 ZN.24: 2 residues within 4Å: Chain B: H.261, E.265 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.261, B:E.265, B:E.265

4 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.4: 2 residues within 4Å: Chain A: G.412, N.413 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.413 Water bridges: A:N.413, A:N.413 NAG.5: 2 residues within 4Å: Chain A: E.452, N.454 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.452 NAG.25: 2 residues within 4Å: Chain B: G.412, N.413 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.413 Water bridges: B:N.413, B:N.413 NAG.26: 2 residues within 4Å: Chain B: E.452, N.454 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.452

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

PGE.6: 6 residues within 4Å: Chain A: Y.67, Y.118, W.276, F.327, Y.331 Ligands: EDO.8 3 PLIP interactions: 3 interactions with chain A Water bridges: A:Y.118, A:Y.118, A:Y.118 PGE.27: 6 residues within 4Å: Chain B: Y.67, Y.118, W.276, F.327, Y.331 Ligands: EDO.29 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Y.118

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 4 residues within 4Å: Chain A: M.80, Y.439, E.442, Y.455 3 PLIP interactions: 3 interactions with chain A Water bridges: A:N.426, A:N.426, A:E.442 GOL.12: 4 residues within 4Å: Chain A: H.156, V.235, A.236, R.239 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.156, A:R.239, A:R.239 GOL.17: 0 residues within 4Å: (No contacts) 3 PLIP interactions: 3 interactions with chain A Water bridges: A:K.343, A:S.345, A:D.348 GOL.28: 4 residues within 4Å: Chain B: M.80, Y.439, E.442, Y.455 3 PLIP interactions: 3 interactions with chain B Water bridges: B:N.426, B:N.426, B:Y.455 GOL.33: 4 residues within 4Å: Chain B: H.156, V.235, A.236, R.239 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:H.156, B:R.239, B:R.239 GOL.38: 0 residues within 4Å: (No contacts) 3 PLIP interactions: 3 interactions with chain B Water bridges: B:K.343, B:D.348, B:D.348

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

EDO.8: 5 residues within 4Å: Chain A: W.81, E.196, F.327, H.437 Ligands: PGE.6 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:W.81, A:E.196 Water bridges: A:S.197 EDO.10: 5 residues within 4Å: Chain A: K.343, N.379, N.380, G.381, I.382 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.343, A:N.380, A:G.381, A:I.382 EDO.11: 4 residues within 4Å: Chain A: Y.331, G.332, A.333, P.334 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.331 Water bridges: A:A.333 EDO.14: 6 residues within 4Å: Chain A: K.322, D.323, R.385, E.431, W.432, G.434 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.322, A:R.385 Water bridges: A:R.385, A:W.432, A:M.433 EDO.15: 6 residues within 4Å: Chain A: R.423, L.427, V.428, W.429, P.430, E.431 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.428 Water bridges: A:E.431 EDO.16: 7 residues within 4Å: Chain A: R.41, E.89, R.264, E.265, K.266, K.267, P.268 2 PLIP interactions: 2 interactions with chain A Water bridges: A:G.38, A:R.41 EDO.18: 4 residues within 4Å: Chain A: F.419, D.501, H.510, L.513 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.501 EDO.29: 5 residues within 4Å: Chain B: W.81, E.196, F.327, H.437 Ligands: PGE.27 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:W.81, B:E.196 Water bridges: B:S.197 EDO.31: 5 residues within 4Å: Chain B: K.343, N.379, N.380, G.381, I.382 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:K.343, B:N.380, B:G.381, B:I.382 EDO.32: 4 residues within 4Å: Chain B: Y.331, G.332, A.333, P.334 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Y.331 Water bridges: B:A.333 EDO.35: 6 residues within 4Å: Chain B: K.322, D.323, R.385, E.431, W.432, G.434 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:K.322, B:D.323, B:R.385 Water bridges: B:R.385 EDO.36: 6 residues within 4Å: Chain B: R.423, L.427, V.428, W.429, P.430, E.431 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:V.428 Water bridges: B:E.431 EDO.37: 7 residues within 4Å: Chain B: R.41, E.89, R.264, E.265, K.266, K.267, P.268 3 PLIP interactions: 3 interactions with chain B Water bridges: B:G.38, B:R.41, B:E.89 EDO.39: 4 residues within 4Å: Chain B: F.419, D.501, H.510, L.513 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.501

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

PEG.9: 2 residues within 4Å: Chain A: N.84, R.85 1 PLIP interactions: 1 interactions with chain A Water bridges: A:E.86 PEG.13: 1 residues within 4Å: Chain A: K.343 No protein-ligand interaction detected (PLIP) PEG.30: 2 residues within 4Å: Chain B: N.84, R.85 1 PLIP interactions: 1 interactions with chain B Water bridges: B:E.86 PEG.34: 1 residues within 4Å: Chain B: K.343 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Silman, I. et al., Torpedo californica acetylcholinesterase is stabilized by binding of a divalent metal ion to a novel and versatile 4D motif. Protein Sci. (2021)

Release Date

2021-03-17

Peptides

Acetylcholinesterase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Acetylcholinesterase

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