SMTL ID : 1w9d.1

S. alba myrosinase in complex with S-ethyl phenylacetothiohydroximate- O-sulfate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

monomer

Ligands

2 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.1: 5 residues within 4Å: Chain A: S.207, N.218, T.221, E.305, T.345 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 7 residues within 4Å: Chain A: Y.264, N.265, D.266, N.361, A.362, S.363, H.365 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- BMA- XYP- FUC: beta-D-xylopyranose-(1-2)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-XYP-FUC.2: 5 residues within 4Å: Chain A: N.265, T.267, D.268, A.362, S.363 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- BMA- XYP- MAN- MAN- FUC: beta-D-xylopyranose-(1-2)-[alpha-D-mannopyranose-(1-3)][alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-XYP-MAN-MAN-FUC.3: 4 residues within 4Å: Chain A: N.292, T.294, Q.297, I.300 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.297, A:Q.297, A:Q.297

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

NAG.5: 6 residues within 4Å: Chain A: T.17, D.18, A.19, N.21, S.24, P.501 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:P.501 Hydrogen bonds: A:D.18, A:N.21, A:N.21 Water bridges: A:A.19, A:S.24 NAG.6: 2 residues within 4Å: Chain A: N.90, S.500 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.90, A:S.500 NAG.7: 4 residues within 4Å: Chain A: K.165, D.239, L.240, N.244 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.239, A:N.244 Water bridges: A:N.244 NAG.8: 2 residues within 4Å: Chain A: N.60, S.213 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.60 Water bridges: A:N.60, A:S.213, A:S.213 NAG.9: 2 residues within 4Å: Chain A: N.346, M.351 No protein-ligand interaction detected (PLIP) NAG.10: 2 residues within 4Å: Chain A: N.482, D.485 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.485 Water bridges: A:T.484, A:D.485

1 x SEH: S-BENZYL PHENYLACETOTHIOHYDROXIMATE-O-SULFATE(Non-covalent)

SEH.11: 12 residues within 4Å: Chain A: Q.187, Y.189, S.190, R.194, I.257, R.259, F.282, Y.330, F.331, F.371, E.372 Ligands: GOL.19 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:Y.330, A:F.371 Hydrogen bonds: A:Q.187, A:R.194 Water bridges: A:R.259, A:R.259, A:R.259, A:R.259 Salt bridges: A:R.259 pi-Stacking: A:Y.330, A:F.331

1 x ZN: ZINC ION(Non-covalent)

ZN.12: 2 residues within 4Å: Chain A: H.56, D.70 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.56, A:D.70, A:D.70

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

SO4.13: 3 residues within 4Å: Chain A: E.153, R.205, A.216 5 PLIP interactions: 5 interactions with chain A Water bridges: A:E.153, A:R.205, A:R.205, A:R.205 Salt bridges: A:R.205 SO4.14: 2 residues within 4Å: Chain A: K.108, R.111 2 PLIP interactions: 2 interactions with chain A Water bridges: A:R.111 Salt bridges: A:R.111 SO4.15: 3 residues within 4Å: Chain A: R.259, Q.333, L.357 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:Q.333, A:Q.333 Water bridges: A:R.259, A:Y.359, A:Y.359, A:Y.359 Salt bridges: A:R.259 SO4.16: 4 residues within 4Å: Chain A: C.6, Q.7, E.8, N.9 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.8, A:N.9, A:N.9

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.17: 8 residues within 4Å: Chain A: G.53, F.54, R.57, Q.146, Q.149, D.150, P.203, Y.215 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.57, A:Q.146 GOL.18: 3 residues within 4Å: Chain A: H.247, Q.248, G.249 1 PLIP interactions: 1 interactions with chain A Water bridges: A:K.180 GOL.19: 9 residues within 4Å: Chain A: Q.39, H.141, N.186, Q.187, E.409, W.457, E.464, F.465 Ligands: SEH.11 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Q.39, A:Q.39, A:N.186, A:Q.187, A:N.328, A:E.464

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bourderioux, A. et al., The Glucosinolate-Myrosinase System. New Insights Into Enzyme-Substrate Interactions by Use of Simplified Inhibitors. Org.Biomol.Chem. (2005)

Release Date

2005-05-19

Peptides

GLYCOSIDASE: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
M

GLYCOSIDASE

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