SMTL ID : 7r0a.1

Structure of sarin phosphonylated acetylcholinesterase in complex with 2-((hydroxyimino)methyl)-1-(5-(4-methyl-3-nitrobenzamido)pentyl)pyridinium

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

homo-dimer

Ligands

2 x I4H: ~{N}-ethyl-4-methyl-3-nitro-benzamide(Non-covalent)

I4H.1: 8 residues within 4Å: Chain A: Y.72, Y.124, W.286, I.294, F.295, R.296, F.338, Y.341 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:Y.341 Hydrogen bonds: A:Y.72 pi-Stacking: A:W.286 I4H.9: 8 residues within 4Å: Chain B: Y.72, Y.124, W.286, I.294, F.295, R.296, F.338, Y.341 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:W.286, B:W.286, B:Y.341 Hydrogen bonds: B:Y.72

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

NAG.2: 4 residues within 4Å: Chain A: G.345, S.347, N.350, L.353 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.345 Water bridges: A:G.345 NAG.3: 1 residues within 4Å: Chain A: N.464 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.464 NAG.10: 4 residues within 4Å: Chain B: G.345, S.347, N.350, L.353 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:G.345, B:S.347

5 x PG0: 2-(2-METHOXYETHOXY)ETHANOL(Non-functional Binders)

PG0.4: 3 residues within 4Å: Chain A: V.303, G.305, S.309 No protein-ligand interaction detected (PLIP) PG0.5: 3 residues within 4Å: Chain A: H.381, Y.382 Chain B: Q.527 No protein-ligand interaction detected (PLIP) PG0.7: 5 residues within 4Å: Chain A: I.20, L.33, T.63, T.64, R.136 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.136 PG0.11: 4 residues within 4Å: Chain B: V.303, D.304, G.305, S.309 No protein-ligand interaction detected (PLIP) PG0.12: 5 residues within 4Å: Chain B: K.332, D.333, D.396, L.441, W.442 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.332

1 x P15: 2,5,8,11,14,17-HEXAOXANONADECAN-19-OL(Non-covalent)

P15.6: 12 residues within 4Å: Chain A: A.377, L.380, H.381, Q.527, F.531, F.535 Chain B: A.377, L.380, H.381, Q.527, F.531, F.535 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:Q.527, B:Q.527

3 x TOE: 2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXYL(Non-covalent)

TOE.8: 6 residues within 4Å: Chain A: D.333, E.351, R.395, D.396, L.441, W.442 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.351, A:R.395 TOE.13: 5 residues within 4Å: Chain B: R.11, R.13, E.185, A.188, A.189 No protein-ligand interaction detected (PLIP) TOE.14: 4 residues within 4Å: Chain A: Q.527 Chain B: H.381, Y.382, D.384 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lindgren, C. et al., Broad-Spectrum Antidote Discovery by Untangling the Reactivation Mechanism of Nerve-Agent-Inhibited Acetylcholinesterase. Chemistry (2022)

Release Date

2022-04-27

Peptides

Acetylcholinesterase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Acetylcholinesterase

Related Entries With Identical Sequence