SMTL ID : 5dlp.1

Acetylcholinesterase Methylene Blue no PEG

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.70 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: 2 residues within 4Å: Chain A: N.59, S.61 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.59, A:S.61 NAG-FUC.20: 2 residues within 4Å: Chain B: N.59, S.61 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.59, B:S.61

2 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.2: 2 residues within 4Å: Chain A: E.455, N.457 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.21: 2 residues within 4Å: Chain B: E.455, N.457 No protein-ligand interaction detected (PLIP)

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

MBT.3: 7 residues within 4Å: Chain A: Y.70, W.84, Y.121, W.279, F.330, F.331, Y.334 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:Y.70, A:F.330, A:F.331 pi-Stacking: A:W.279, A:Y.334 MBT.22: 7 residues within 4Å: Chain B: Y.70, W.84, Y.121, W.279, F.330, F.331, Y.334 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:Y.70, B:F.330, B:F.331 pi-Stacking: B:W.279, B:Y.334

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

NAG.4: 1 residues within 4Å: Chain A: N.416 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.416 NAG.23: 1 residues within 4Å: Chain B: N.416 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.416

30 x SO4: SULFATE ION(Non-functional Binders)

SO4.5: 3 residues within 4Å: Chain A: S.237, A.239, R.243 Ligand excluded by PLIP SO4.6: 4 residues within 4Å: Chain A: K.346, N.382, N.383, G.384 Ligand excluded by PLIP SO4.7: 3 residues within 4Å: Chain A: H.513, Q.514 Chain B: M.379 Ligand excluded by PLIP SO4.8: 4 residues within 4Å: Chain A: P.106, K.107, S.108, T.109 Ligand excluded by PLIP SO4.9: 4 residues within 4Å: Chain A: H.406, N.409, N.525, Q.526 Ligand excluded by PLIP SO4.10: 5 residues within 4Å: Chain A: N.424, H.425, N.506, T.507, E.508 Ligand excluded by PLIP SO4.11: 3 residues within 4Å: Chain A: T.459, A.460, E.461 Ligand excluded by PLIP SO4.12: 5 residues within 4Å: Chain A: P.21, V.22, L.23, K.133, Y.134 Ligand excluded by PLIP SO4.13: 6 residues within 4Å: Chain A: R.289, S.359, V.360, P.361, H.362, H.398 Ligand excluded by PLIP SO4.14: 2 residues within 4Å: Chain A: P.433, E.434 Ligand excluded by PLIP SO4.15: 6 residues within 4Å: Chain A: Q.68, M.90, S.91, E.92, D.93, P.271 Ligand excluded by PLIP SO4.16: 3 residues within 4Å: Chain A: D.342, S.343, E.344 Ligand excluded by PLIP SO4.17: 2 residues within 4Å: Chain A: S.490, K.491 Ligand excluded by PLIP SO4.18: 4 residues within 4Å: Chain A: R.220, R.221, Q.318, N.416 Ligand excluded by PLIP SO4.19: 1 residues within 4Å: Chain A: N.382 Ligand excluded by PLIP SO4.24: 3 residues within 4Å: Chain B: S.237, A.239, R.243 Ligand excluded by PLIP SO4.25: 4 residues within 4Å: Chain B: K.346, N.382, N.383, G.384 Ligand excluded by PLIP SO4.26: 3 residues within 4Å: Chain A: M.379 Chain B: H.513, Q.514 Ligand excluded by PLIP SO4.27: 4 residues within 4Å: Chain B: P.106, K.107, S.108, T.109 Ligand excluded by PLIP SO4.28: 4 residues within 4Å: Chain B: H.406, N.409, N.525, Q.526 Ligand excluded by PLIP SO4.29: 5 residues within 4Å: Chain B: N.424, H.425, N.506, T.507, E.508 Ligand excluded by PLIP SO4.30: 3 residues within 4Å: Chain B: T.459, A.460, E.461 Ligand excluded by PLIP SO4.31: 5 residues within 4Å: Chain B: P.21, V.22, L.23, K.133, Y.134 Ligand excluded by PLIP SO4.32: 6 residues within 4Å: Chain B: R.289, S.359, V.360, P.361, H.362, H.398 Ligand excluded by PLIP SO4.33: 2 residues within 4Å: Chain B: P.433, E.434 Ligand excluded by PLIP SO4.34: 6 residues within 4Å: Chain B: Q.68, M.90, S.91, E.92, D.93, P.271 Ligand excluded by PLIP SO4.35: 3 residues within 4Å: Chain B: D.342, S.343, E.344 Ligand excluded by PLIP SO4.36: 2 residues within 4Å: Chain B: S.490, K.491 Ligand excluded by PLIP SO4.37: 4 residues within 4Å: Chain B: R.220, R.221, Q.318, N.416 Ligand excluded by PLIP SO4.38: 1 residues within 4Å: Chain B: N.382 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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