SMTL ID : 5hf9.1

Crystal structure of human acetylcholinesterase in complex with paraoxon and HI6

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-dimer

Ligands

2 x NAG- NAG- FUC: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-FUC.1: 5 residues within 4Å: Chain A: P.343, G.344, F.345, S.346, N.349 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.346, A:G.344 NAG-NAG-FUC.2: 6 residues within 4Å: Chain B: A.342, P.343, G.344, S.346, D.348, N.349 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:D.348 Hydrogen bonds: B:S.346, B:G.344

2 x DEP: DIETHYL PHOSPHONATE(Covalent)

DEP.3: 11 residues within 4Å: Chain A: G.119, G.120, G.121, S.202, A.203, W.235, F.294, F.296, F.337, H.446 Ligands: HI6.6 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:W.235, A:F.294 Hydrogen bonds: A:G.120, A:G.121, A:A.203 Salt bridges: A:H.446 DEP.8: 9 residues within 4Å: Chain B: G.119, G.120, G.121, S.202, A.203, W.235, F.294, F.296, H.446 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:W.235, B:F.294 Hydrogen bonds: B:G.120, B:G.121, B:A.203 Salt bridges: B:H.446

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

EDO.4: 8 residues within 4Å: Chain A: Y.381, T.382, D.383, H.386, P.387, R.392, L.393, A.396 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.381, A:D.383, A:H.386 EDO.5: 4 residues within 4Å: Chain A: Q.507, A.525, A.529, R.533 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.507, A:R.533 Water bridges: A:Q.507 EDO.10: 8 residues within 4Å: Chain B: Y.381, T.382, D.383, H.386, P.387, R.392, L.393, A.396 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Y.381, B:D.383, B:H.386 EDO.11: 5 residues within 4Å: Chain A: W.384 Chain B: Q.507, A.525, A.529, R.533 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:Q.507, B:R.533, B:R.533 Water bridges: B:Q.507, B:N.532

2 x HI6: 4-(AMINOCARBONYL)-1-[({2-[(E)-(HYDROXYIMINO)METHYL]PYRIDINIUM-1-YL}METHOXY)METHYL]PYRIDINIUM(Non-covalent)

HI6.6: 11 residues within 4Å: Chain A: Y.71, D.73, Y.123, V.281, E.284, W.285, V.293, F.294, Y.336, Y.340 Ligands: DEP.3 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:Y.71, A:W.285, A:Y.336 Hydrogen bonds: A:E.284, A:W.285, A:F.294 Water bridges: A:S.292, A:R.295 pi-Stacking: A:Y.71, A:Y.123, A:W.285, A:W.285, A:Y.340 HI6.13: 8 residues within 4Å: Chain B: Y.71, D.73, Y.123, V.281, E.284, W.285, Y.336, Y.340 15 PLIP interactions: 15 interactions with chain B Hydrophobic interactions: B:Y.71, B:W.285, B:Y.336 Hydrogen bonds: B:D.73, B:Y.123, B:V.281, B:E.284, B:W.285 Water bridges: B:D.73, B:S.124 pi-Stacking: B:Y.71, B:Y.123, B:W.285, B:W.285, B:Y.340

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

NAG.7: 1 residues within 4Å: Chain B: N.264 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.264

1 x PE8: 3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL(Non-covalent)

PE8.9: 7 residues within 4Å: Chain B: G.162, M.240, D.303, G.304, D.305, S.308, D.309 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.309

1 x NO3: NITRATE ION(Non-functional Binders)

NO3.12: 4 residues within 4Å: Chain B: P.161, M.240, G.241, R.244 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:P.161, B:R.244

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Franklin, M.C. et al., Structures of paraoxon-inhibited human acetylcholinesterase reveal perturbations of the acyl loop and the dimer interface. Proteins (2016)

Release Date

2016-06-22

Peptides

Acetylcholinesterase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Acetylcholinesterase

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