SMTL ID : 4b0p.1

Crystal structure of soman-aged human butyrylcholinesterase in complex with methyl 2-(pentafluorobenzyloxyimino)pyridinium

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-dimer

Ligands

4 x NAG- NAG- FUL: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[beta-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose(Non-covalent)(Non-functional Binders)

NAG-NAG-FUL.1: 6 residues within 4Å: Chain A: Y.237, N.241, N.245, L.249, F.278, P.281 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.249 NAG-NAG-FUL.2: 6 residues within 4Å: Chain A: P.335, G.336, F.337, S.338, N.341, N.342 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.338, A:G.336 NAG-NAG-FUL.20: 6 residues within 4Å: Chain B: Y.237, N.241, N.245, L.249, F.278, P.281 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:L.249 NAG-NAG-FUL.21: 6 residues within 4Å: Chain B: P.335, G.336, F.337, S.338, N.341, N.342 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.338, B:G.336

2 x GLY: GLYCINE(Non-covalent)

GLY.3: 5 residues within 4Å: Chain A: L.18, Y.61, W.98, D.129, K.131 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:W.98 Salt bridges: A:K.131 GLY.22: 5 residues within 4Å: Chain B: L.18, Y.61, W.98, D.129, K.131 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:W.98 Salt bridges: B:K.131

4 x NA: SODIUM ION(Non-functional Binders)

NA.4: 3 residues within 4Å: Chain B: E.80, N.83 Ligands: NA.23 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.80, B:N.83 NA.11: 3 residues within 4Å: Chain A: M.81, Y.440, E.443 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.443 NA.23: 3 residues within 4Å: Chain A: E.80, N.83 Ligands: NA.4 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.80, A:N.83 Water bridges: A:E.80 NA.30: 3 residues within 4Å: Chain B: M.81, Y.440, E.443 No protein-ligand interaction detected (PLIP)

2 x K: POTASSIUM ION(Non-covalent)

K.5: 2 residues within 4Å: Chain A: X.198 Ligands: MF5.6 No protein-ligand interaction detected (PLIP) K.24: 2 residues within 4Å: Chain B: X.198 Ligands: MF5.25 No protein-ligand interaction detected (PLIP)

2 x MF5: 1-(1-methylpyridin-1-ium-2-yl)-N-[[2,3,4,5,6-pentakis(fluoranyl)phenyl]methoxy]methanimine(Non-covalent)

MF5.6: 12 residues within 4Å: Chain A: D.70, W.82, G.115, G.116, E.197, P.285, A.328, F.329, Y.332, H.438, G.439 Ligands: K.5 3 PLIP interactions: 3 interactions with chain A pi-Stacking: A:W.82, A:Y.332 Halogen bonds: A:P.285 MF5.25: 12 residues within 4Å: Chain B: D.70, W.82, G.115, G.116, E.197, P.285, A.328, F.329, Y.332, H.438, G.439 Ligands: K.24 3 PLIP interactions: 3 interactions with chain B pi-Stacking: B:W.82, B:Y.332 Halogen bonds: B:P.285

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

NAG.7: 2 residues within 4Å: Chain A: R.14, N.57 No protein-ligand interaction detected (PLIP) NAG.8: 3 residues within 4Å: Chain A: N.106, N.188, K.190 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.188 Water bridges: A:K.190, A:K.190, A:K.190 NAG.9: 4 residues within 4Å: Chain A: R.465, K.469, E.482, N.485 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:R.465, A:K.469, A:E.482 Hydrogen bonds: A:R.465, A:N.485 NAG.10: 1 residues within 4Å: Chain A: N.256 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.256 NAG.26: 2 residues within 4Å: Chain B: R.14, N.57 No protein-ligand interaction detected (PLIP) NAG.27: 3 residues within 4Å: Chain B: N.106, N.188, K.190 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.188 Water bridges: B:K.190, B:K.190, B:K.190 NAG.28: 4 residues within 4Å: Chain B: R.465, K.469, E.482, N.485 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:R.465, B:K.469, B:E.482 Hydrogen bonds: B:R.465, B:N.485 NAG.29: 1 residues within 4Å: Chain B: N.256 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.256

8 x CA: CALCIUM ION(Non-covalent)

CA.12: 2 residues within 4Å: Chain A: Y.420, R.515 No protein-ligand interaction detected (PLIP) CA.13: 3 residues within 4Å: Chain A: S.487, T.488, T.508 No protein-ligand interaction detected (PLIP) CA.18: 4 residues within 4Å: Chain A: C.66, P.269, Q.270, L.273 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:C.66 CA.19: 4 residues within 4Å: Chain A: P.189, S.215, F.217, T.218 No protein-ligand interaction detected (PLIP) CA.31: 2 residues within 4Å: Chain B: Y.420, R.515 No protein-ligand interaction detected (PLIP) CA.32: 3 residues within 4Å: Chain B: S.487, T.488, T.508 No protein-ligand interaction detected (PLIP) CA.37: 4 residues within 4Å: Chain B: C.66, P.269, Q.270, L.273 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:C.66 CA.38: 4 residues within 4Å: Chain B: P.189, S.215, F.217, T.218 No protein-ligand interaction detected (PLIP)

8 x CL: CHLORIDE ION(Non-functional Binders)

CL.14: 2 residues within 4Å: Chain A: R.242, V.288 Ligand excluded by PLIP CL.15: 2 residues within 4Å: Chain A: R.347, Q.351 Ligand excluded by PLIP CL.16: 2 residues within 4Å: Chain A: T.512, K.513 Ligand excluded by PLIP CL.17: 1 residues within 4Å: Chain A: R.515 Ligand excluded by PLIP CL.33: 2 residues within 4Å: Chain B: R.242, V.288 Ligand excluded by PLIP CL.34: 2 residues within 4Å: Chain B: R.347, Q.351 Ligand excluded by PLIP CL.35: 2 residues within 4Å: Chain B: T.512, K.513 Ligand excluded by PLIP CL.36: 1 residues within 4Å: Chain B: R.515 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wandhammer, M. et al., A Step Toward the Reactivation of Aged Cholinesterases -Crystal Structure of Ligands Binding to Aged Human Butyrylcholinesterase. Chem.Biol.Interact (2013)

Release Date

2012-08-29

Peptides

CHOLINESTERASE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

CHOLINESTERASE

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