SMTL ID : 5e4t.1

Acetylcholinesterase Methylene Blue with PEG

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.43 Å

Oligo State

homo-dimer

Ligands

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

NAG-FUC.1: 4 residues within 4Å: Chain A: N.59, S.61, T.62 Ligands: PGE.18 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.59, A:S.61

1 x NAG- NAG- BMA- MAN: alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN.2: 1 residues within 4Å: Chain A: N.416 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- BMA- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-MAN.3: 3 residues within 4Å: Chain A: E.455, L.456, N.457 No protein-ligand interaction detected (PLIP)

2 x MBT: 3,7-BIS(DIMETHYLAMINO)PHENOTHIAZIN-5-IUM(Non-covalent)

MBT.4: 9 residues within 4Å: Chain A: Y.70, Y.121, W.279, F.330, F.331, Y.334 Ligands: PEG.6, PGE.17, PGE.21 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:W.279, A:Y.334, A:Y.334 pi-Stacking: A:W.279, A:W.279, A:W.279 MBT.31: 9 residues within 4Å: Chain B: Y.70, Y.121, W.279, F.330, F.331, Y.334 Ligands: PEG.33, PGE.44, PGE.48 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:W.279, B:Y.334, B:Y.334 pi-Stacking: B:W.279, B:W.279, B:W.279

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

PEG.5: 5 residues within 4Å: Chain A: N.230, P.232, S.235, S.237 Ligands: EDO.23 Ligand excluded by PLIP PEG.6: 5 residues within 4Å: Chain A: Y.70, Q.74, Y.334, G.335 Ligands: MBT.4 Ligand excluded by PLIP PEG.7: 3 residues within 4Å: Chain A: I.296, D.297, G.298 Ligand excluded by PLIP PEG.8: 6 residues within 4Å: Chain A: R.105, P.106, K.107, Q.185, F.186 Ligands: PEG.13 Ligand excluded by PLIP PEG.9: 4 residues within 4Å: Chain A: F.422, N.424, H.513, R.517 Ligand excluded by PLIP PEG.10: 7 residues within 4Å: Chain A: K.325, D.326, D.389, D.393, E.434, W.435 Ligands: EDO.22 Ligand excluded by PLIP PEG.11: 4 residues within 4Å: Chain A: V.20, Y.63, W.100, N.131 Ligand excluded by PLIP PEG.12: 3 residues within 4Å: Chain A: L.7, K.14, V.57 Ligand excluded by PLIP PEG.13: 2 residues within 4Å: Chain A: R.105 Ligands: PEG.8 Ligand excluded by PLIP PEG.14: 4 residues within 4Å: Chain A: K.346, I.347, S.348, N.382 Ligand excluded by PLIP PEG.15: 2 residues within 4Å: Chain A: P.493, L.494 Ligand excluded by PLIP PEG.16: 1 residues within 4Å: Chain A: P.53 Ligand excluded by PLIP PEG.32: 5 residues within 4Å: Chain B: N.230, P.232, S.235, S.237 Ligands: EDO.50 Ligand excluded by PLIP PEG.33: 5 residues within 4Å: Chain B: Y.70, Q.74, Y.334, G.335 Ligands: MBT.31 Ligand excluded by PLIP PEG.34: 3 residues within 4Å: Chain B: I.296, D.297, G.298 Ligand excluded by PLIP PEG.35: 6 residues within 4Å: Chain B: R.105, P.106, K.107, Q.185, F.186 Ligands: PEG.40 Ligand excluded by PLIP PEG.36: 4 residues within 4Å: Chain B: F.422, N.424, H.513, R.517 Ligand excluded by PLIP PEG.37: 7 residues within 4Å: Chain B: K.325, D.326, D.389, D.393, E.434, W.435 Ligands: EDO.49 Ligand excluded by PLIP PEG.38: 4 residues within 4Å: Chain B: V.20, Y.63, W.100, N.131 Ligand excluded by PLIP PEG.39: 3 residues within 4Å: Chain B: L.7, K.14, V.57 Ligand excluded by PLIP PEG.40: 2 residues within 4Å: Chain B: R.105 Ligands: PEG.35 Ligand excluded by PLIP PEG.41: 4 residues within 4Å: Chain B: K.346, I.347, S.348, N.382 Ligand excluded by PLIP PEG.42: 2 residues within 4Å: Chain B: P.493, L.494 Ligand excluded by PLIP PEG.43: 1 residues within 4Å: Chain B: P.53 Ligand excluded by PLIP

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

PGE.17: 10 residues within 4Å: Chain A: W.84, G.117, G.118, G.119, Y.121, Y.130, E.199, F.331, H.440 Ligands: MBT.4 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:G.117, A:G.118, A:Y.130, A:S.200, A:S.200 Water bridges: A:G.119, A:S.122 PGE.18: 5 residues within 4Å: Chain A: V.57, W.58, N.59 Ligands: NAG-FUC.1, NAG-FUC.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.59 PGE.19: 4 residues within 4Å: Chain A: E.499, K.501, V.512, Q.514 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.501 PGE.20: 5 residues within 4Å: Chain A: R.243, E.247, N.280, V.281, L.282 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.243, A:R.243, A:L.282 PGE.21: 6 residues within 4Å: Chain A: W.279, D.285, S.286, Y.334, G.335 Ligands: MBT.4 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:W.279 Water bridges: A:D.285, A:D.285 PGE.44: 10 residues within 4Å: Chain B: W.84, G.117, G.118, G.119, Y.121, Y.130, E.199, F.331, H.440 Ligands: MBT.31 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:G.117, B:G.118, B:S.200, B:S.200 Water bridges: B:G.119, B:S.122, B:E.199 PGE.45: 3 residues within 4Å: Chain B: V.57, W.58, N.59 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.59 PGE.46: 4 residues within 4Å: Chain B: E.499, K.501, V.512, Q.514 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.501 PGE.47: 5 residues within 4Å: Chain B: R.243, E.247, N.280, V.281, L.282 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.243, B:R.243, B:L.282 PGE.48: 6 residues within 4Å: Chain B: W.279, D.285, S.286, Y.334, G.335 Ligands: MBT.31 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:W.279 Water bridges: B:D.285, B:D.285

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

EDO.22: 4 residues within 4Å: Chain A: E.344, I.385, R.388 Ligands: PEG.10 Ligand excluded by PLIP EDO.23: 5 residues within 4Å: Chain A: P.232, R.289, P.361, H.362 Ligands: PEG.5 Ligand excluded by PLIP EDO.24: 4 residues within 4Å: Chain A: K.11, G.13, P.53, W.54 Ligand excluded by PLIP EDO.25: 3 residues within 4Å: Chain A: R.426, V.431, W.432 Ligand excluded by PLIP EDO.26: 4 residues within 4Å: Chain A: T.109, E.139, E.140, K.478 Ligand excluded by PLIP EDO.27: 3 residues within 4Å: Chain A: Y.375, T.376 Chain B: Q.519 Ligand excluded by PLIP EDO.28: 4 residues within 4Å: Chain A: R.44, E.268, K.269, P.271 Ligand excluded by PLIP EDO.29: 3 residues within 4Å: Chain A: S.55, V.57, W.58 Ligand excluded by PLIP EDO.30: 3 residues within 4Å: Chain A: E.306, H.406, N.525 Ligand excluded by PLIP EDO.49: 4 residues within 4Å: Chain B: E.344, I.385, R.388 Ligands: PEG.37 Ligand excluded by PLIP EDO.50: 5 residues within 4Å: Chain B: P.232, R.289, P.361, H.362 Ligands: PEG.32 Ligand excluded by PLIP EDO.51: 4 residues within 4Å: Chain B: K.11, G.13, P.53, W.54 Ligand excluded by PLIP EDO.52: 3 residues within 4Å: Chain B: R.426, V.431, W.432 Ligand excluded by PLIP EDO.53: 4 residues within 4Å: Chain B: T.109, E.139, E.140, K.478 Ligand excluded by PLIP EDO.54: 3 residues within 4Å: Chain A: Q.519 Chain B: Y.375, T.376 Ligand excluded by PLIP EDO.55: 4 residues within 4Å: Chain B: R.44, E.268, K.269, P.271 Ligand excluded by PLIP EDO.56: 3 residues within 4Å: Chain B: S.55, V.57, W.58 Ligand excluded by PLIP EDO.57: 3 residues within 4Å: Chain B: E.306, H.406, N.525 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dym, O. et al., The impact of crystallization conditions on structure-based drug design: A case study on the methylene blue/acetylcholinesterase complex. Protein Sci. (2016)

Release Date

2016-03-30

Peptides

Acetylcholinesterase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Acetylcholinesterase

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