SMTL ID : 6r6w.1

Structure of recombinant human butyrylcholinesterase in complex with a fluorescent NBD-based probe

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.47 Å

Oligo State

monomer

Ligands

1 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: R.11, N.54 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.11, A:N.54

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.2: 4 residues within 4Å: Chain A: P.332, G.333, S.335, N.338 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.335, A:S.335 NAG-NAG-FUC.3: 6 residues within 4Å: Chain A: N.238, N.242, L.246, F.275, V.277, P.278 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.246 Hydrogen bonds: A:V.277

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

NAG.4: 3 residues within 4Å: Chain A: N.103, N.185, K.187 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.185, A:K.187 NAG.5: 2 residues within 4Å: Chain A: N.253, E.256 No protein-ligand interaction detected (PLIP) NAG.6: 4 residues within 4Å: Chain A: R.462, K.466, E.479, N.482 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:K.466 Hydrogen bonds: A:R.462, A:N.482

1 x JUB: [7-[4-[2-[naphthalen-2-ylsulfonyl-[[(3~{S})-1-(phenylmethyl)piperidin-1-ium-3-yl]methyl]amino]ethyl]piperazin-4-ium-1-yl]-2,1,3-benzoxadiazol-4-yl]-oxidanyl-oxidanylidene-azanium(Non-covalent)

JUB.7: 21 residues within 4Å: Chain A: D.67, W.79, G.113, G.114, Q.116, T.117, S.195, W.228, P.282, L.283, S.284, V.285, A.325, F.326, Y.329, F.395, W.427, M.434, H.435, Y.437 Ligands: DMS.14 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:W.228, A:V.285, A:A.325, A:F.326, A:F.395, A:W.427, A:Y.437 pi-Stacking: A:W.79, A:W.228, A:W.228

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.8: 1 residues within 4Å: Chain A: R.216 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.216, A:R.216, A:Q.313

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

SO4.9: 4 residues within 4Å: Chain A: Q.313, G.410, N.411, N.412 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.313, A:N.411, A:N.412 SO4.10: 6 residues within 4Å: Chain A: W.228, T.231, R.239, L.283, S.284, V.285 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.283, A:V.285 Salt bridges: A:R.239 SO4.11: 6 residues within 4Å: Chain A: R.467, Q.483, S.484, T.485, S.504, T.505 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:R.467, A:T.485, A:T.485, A:T.485, A:T.505, A:T.505 Water bridges: A:S.463, A:S.463, A:S.463 SO4.12: 2 residues within 4Å: Chain A: R.344, Q.348 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.348, A:Q.348 Salt bridges: A:R.344 SO4.13: 3 residues within 4Å: Chain A: K.320, Y.417, R.512 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.417 Salt bridges: A:K.320, A:R.512

1 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.14: 7 residues within 4Å: Chain A: G.112, G.113, E.194, S.195, H.435, G.436 Ligands: JUB.7 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:E.194 pi-Cation interactions: A:W.79

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pajk, S. et al., Development of potent reversible selective inhibitors of butyrylcholinesterase as fluorescent probes. J Enzyme Inhib Med Chem (2020)

Release Date

2020-01-15

Peptides

Cholinesterase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Cholinesterase

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