SMTL ID : 6g17.1

Non-aged form of Torpedo californica acetylcholinesterase inhibited by nerve agent tabun

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-dimer

Ligands

2 x NTJ: R-ETHYL N,N-DIMETHYLPHOSPHONAMIDATE(Covalent)

NTJ.1: 11 residues within 4Å: Chain A: G.117, G.118, G.119, S.200, A.201, W.233, F.288, F.290, F.331, H.440 Ligands: PEG.10 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.118, A:G.119, A:A.201 NTJ.13: 11 residues within 4Å: Chain B: G.117, G.118, G.119, S.200, A.201, W.233, F.288, F.290, F.331, H.440 Ligands: PEG.22 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:G.118, B:G.119, B:A.201

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

NAG.2: 1 residues within 4Å: Chain A: N.416 2 PLIP interactions: 2 interactions with chain A Water bridges: A:N.416, A:N.416 NAG.3: 3 residues within 4Å: Chain A: N.59, S.61, T.62 No protein-ligand interaction detected (PLIP) NAG.14: 1 residues within 4Å: Chain B: N.416 2 PLIP interactions: 2 interactions with chain B Water bridges: B:N.416, B:N.416 NAG.15: 3 residues within 4Å: Chain B: N.59, S.61, T.62 No protein-ligand interaction detected (PLIP)

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

EDO.4: 4 residues within 4Å: Chain A: R.220, R.221, T.317, Q.318 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.220, A:R.220, A:R.221, A:Q.318 EDO.6: 5 residues within 4Å: Chain A: Y.121, F.330, F.331, Y.334 Ligands: PEG.10 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:F.330 Water bridges: A:Y.121 EDO.7: 4 residues within 4Å: Chain A: R.44, R.267, E.268, K.269 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.44 Water bridges: A:R.44, A:E.92 EDO.16: 4 residues within 4Å: Chain B: R.220, R.221, T.317, Q.318 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:R.220, B:R.220, B:R.221, B:T.317, B:Q.318 EDO.18: 5 residues within 4Å: Chain B: Y.121, F.330, F.331, Y.334 Ligands: PEG.22 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:F.330 Water bridges: B:Y.121 EDO.19: 4 residues within 4Å: Chain B: R.44, R.267, E.268, K.269 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.44 Water bridges: B:R.44, B:E.92

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

PGE.5: 3 residues within 4Å: Chain A: Y.70, Y.121, W.279 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.121 Water bridges: A:Y.121, A:D.276 PGE.17: 3 residues within 4Å: Chain B: Y.70, Y.121, W.279 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Y.121 Water bridges: B:Y.70, B:Y.121, B:D.276

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

PEG.8: 6 residues within 4Å: Chain A: T.10, K.11, G.13, P.53, W.54 Ligands: PEG.11 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:W.54 PEG.9: 6 residues within 4Å: Chain A: R.105, P.106, K.107, Q.185, F.186, G.188 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.105, A:K.107, A:K.107 PEG.10: 9 residues within 4Å: Chain A: W.84, G.117, G.118, E.199, S.200, F.330, H.440 Ligands: NTJ.1, EDO.6 1 PLIP interactions: 1 interactions with chain A Water bridges: A:G.117 PEG.11: 4 residues within 4Å: Chain A: N.9, T.10, F.186 Ligands: PEG.8 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.9 PEG.12: 4 residues within 4Å: Chain A: F.422, D.504, H.513, L.516 3 PLIP interactions: 3 interactions with chain A Water bridges: A:N.424, A:N.424, A:R.517 PEG.20: 6 residues within 4Å: Chain B: T.10, K.11, G.13, P.53, W.54 Ligands: PEG.23 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:W.54 PEG.21: 6 residues within 4Å: Chain B: R.105, P.106, K.107, Q.185, F.186, G.188 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.105, B:K.107, B:K.107 PEG.22: 9 residues within 4Å: Chain B: W.84, G.117, G.118, E.199, S.200, F.330, H.440 Ligands: NTJ.13, EDO.18 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.200 Water bridges: B:G.117 PEG.23: 4 residues within 4Å: Chain B: N.9, T.10, F.186 Ligands: PEG.20 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.9 PEG.24: 4 residues within 4Å: Chain B: F.422, D.504, H.513, L.516 3 PLIP interactions: 3 interactions with chain B Water bridges: B:N.424, B:N.424, B:R.517

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Santoni, G. et al., Structure-Based Optimization of Nonquaternary Reactivators of Acetylcholinesterase Inhibited by Organophosphorus Nerve Agents. J. Med. Chem. (2018)

Release Date

2018-08-29

Peptides

Acetylcholinesterase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Acetylcholinesterase

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