SMTL ID : 2wxd.1

A MICROMOLAR O-SULFATED THIOHYDROXIMATE INHIBITOR BOUND TO PLANT MYROSINASE

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-dimer

Ligands

8 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: 2 residues within 4Å: Chain A: N.90, S.500 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 5 residues within 4Å: Chain A: S.207, N.218, T.221, E.305, T.345 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 5 residues within 4Å: Chain A: Y.58, N.60, P.212, S.213 Ligands: SO4.19 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 8 residues within 4Å: Chain A: Y.264, N.265, D.266, N.361, A.362, S.363, H.365 Ligands: NAG-NAG-BMA-XYP-FUC.3 No protein-ligand interaction detected (PLIP) NAG-NAG.24: 2 residues within 4Å: Chain B: N.90, S.500 No protein-ligand interaction detected (PLIP) NAG-NAG.25: 5 residues within 4Å: Chain B: S.207, N.218, T.221, E.305, T.345 No protein-ligand interaction detected (PLIP) NAG-NAG.28: 5 residues within 4Å: Chain B: Y.58, N.60, P.212, S.213 Ligands: SO4.42 No protein-ligand interaction detected (PLIP) NAG-NAG.29: 8 residues within 4Å: Chain B: Y.264, N.265, D.266, N.361, A.362, S.363, H.365 Ligands: NAG-NAG-BMA-XYP-FUC.26 No protein-ligand interaction detected (PLIP)

2 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.3: 5 residues within 4Å: Chain A: N.265, T.267, D.268, A.362 Ligands: NAG-NAG.6 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-XYP-FUC.26: 5 residues within 4Å: Chain B: N.265, T.267, D.268, A.362 Ligands: NAG-NAG.29 No protein-ligand interaction detected (PLIP)

2 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.4: 3 residues within 4Å: Chain A: N.292, T.294, Q.297 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.297, A:Q.297, A:Q.297 Water bridges: A:Q.297 NAG-NAG-BMA-XYP-MAN-MAN-FUC.27: 3 residues within 4Å: Chain B: N.292, T.294, Q.297 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.297, B:Q.297, B:Q.297 Water bridges: B:Q.297

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

NAG.7: 6 residues within 4Å: Chain A: T.17, D.18, A.19, N.21, S.24, P.501 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:P.501 Hydrogen bonds: A:D.18, A:N.21 Water bridges: A:A.19 NAG.8: 5 residues within 4Å: Chain A: K.165, D.239, L.240, K.243, N.244 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.240 Water bridges: A:D.239, A:K.243, A:N.244, A:N.244 NAG.9: 1 residues within 4Å: Chain A: N.346 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.346 NAG.10: 3 residues within 4Å: Chain A: N.482, T.484, D.485 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.482, A:D.485 Water bridges: A:T.484, A:D.485 NAG.30: 6 residues within 4Å: Chain B: T.17, D.18, A.19, N.21, S.24, P.501 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:P.501 Hydrogen bonds: B:N.21 Water bridges: B:A.19 NAG.31: 5 residues within 4Å: Chain B: K.165, D.239, L.240, K.243, N.244 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:L.240 Water bridges: B:K.243, B:N.244, B:N.244 NAG.32: 1 residues within 4Å: Chain B: N.346 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.346 NAG.33: 3 residues within 4Å: Chain B: N.482, T.484, D.485 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:N.482, B:D.485 Water bridges: B:T.484, B:D.485, B:D.485

2 x E18: 2-(DIMETHYLAMINO)ETHYL (1Z)-2-PHENYL-N-(SULFOOXY)ETHANIMIDOTHIOATE(Non-covalent)

E18.11: 16 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, E.409, W.457, E.464, F.473 Ligands: SO4.13 10 PLIP interactions: 10 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 Salt bridges: A:R.259, A:E.409, A:E.464 pi-Stacking: A:Y.330, A:F.331 E18.34: 16 residues within 4Å: Chain B: Q.187, Y.189, S.190, R.194, I.257, R.259, F.282, Y.330, F.331, F.371, E.372, E.409, W.457, E.464, F.473 Ligands: SO4.36 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:Y.330, B:F.371 Hydrogen bonds: B:Q.187, B:R.194 Water bridges: B:R.259 Salt bridges: B:R.259, B:E.409, B:E.464 pi-Stacking: B:Y.330, B:F.331

2 x ZN: ZINC ION(Non-covalent)

ZN.12: 5 residues within 4Å: Chain A: H.56, D.70 Chain B: H.56, D.70 Ligands: ZN.35 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain B Metal complexes: A:H.56, A:D.70, B:H.56, B:D.70, B:D.70 ZN.35: 5 residues within 4Å: Chain A: H.56, D.70 Chain B: H.56, D.70 Ligands: ZN.12 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Metal complexes: A:H.56, A:D.70, A:D.70, B:H.56, B:D.70

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

SO4.13: 3 residues within 4Å: Chain A: R.194, R.259 Ligands: E18.11 4 PLIP interactions: 4 interactions with chain A Water bridges: A:R.194, A:R.194 Salt bridges: A:R.194, A:R.259 SO4.14: 3 residues within 4Å: Chain A: E.153, R.205 Chain B: R.106 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Water bridges: A:R.205, A:R.205, A:R.205 Salt bridges: A:R.205 Hydrogen bonds: B:R.106 SO4.15: 2 residues within 4Å: Chain A: K.108, R.111 3 PLIP interactions: 3 interactions with chain A Water bridges: A:R.111, A:R.111 Salt bridges: A:R.111 SO4.16: 4 residues within 4Å: Chain A: C.6, Q.7, E.8, N.9 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.8, A:N.9, A:N.9 Water bridges: A:E.8 SO4.17: 4 residues within 4Å: Chain A: R.269, H.270, A.273, R.277 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.269 Water bridges: A:A.274, A:R.277, A:R.277 Salt bridges: A:H.270, A:R.277 SO4.18: 4 residues within 4Å: Chain A: R.109, V.113, L.170, E.173 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.109 SO4.19: 3 residues within 4Å: Chain A: N.60, H.66 Ligands: NAG-NAG.5 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.60 Salt bridges: A:H.66 SO4.36: 3 residues within 4Å: Chain B: R.194, R.259 Ligands: E18.34 4 PLIP interactions: 4 interactions with chain B Water bridges: B:R.194, B:R.194 Salt bridges: B:R.194, B:R.259 SO4.37: 3 residues within 4Å: Chain A: R.106 Chain B: E.153, R.205 5 PLIP interactions: 1 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:R.106 Water bridges: B:R.205, B:R.205, B:E.222 Salt bridges: B:R.205 SO4.38: 2 residues within 4Å: Chain B: K.108, R.111 3 PLIP interactions: 3 interactions with chain B Water bridges: B:R.111, B:E.151 Salt bridges: B:R.111 SO4.39: 4 residues within 4Å: Chain B: C.6, Q.7, E.8, N.9 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.8, B:N.9, B:N.9 SO4.40: 4 residues within 4Å: Chain B: R.269, H.270, A.273, R.277 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:R.269 Water bridges: B:A.274, B:R.277, B:R.277 Salt bridges: B:H.270, B:R.277 SO4.41: 4 residues within 4Å: Chain B: R.109, V.113, L.170, E.173 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:R.109 SO4.42: 3 residues within 4Å: Chain B: N.60, H.66 Ligands: NAG-NAG.28 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.60 Salt bridges: B:H.66

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.20: 2 residues within 4Å: Chain A: R.269, H.270 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.269, A:R.269 GOL.21: 9 residues within 4Å: Chain A: G.53, F.54, R.57, Y.58, Q.146, Q.149, D.150, P.203, Y.215 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.57, A:Q.146, A:Y.215 Water bridges: A:Y.215 GOL.22: 2 residues within 4Å: Chain A: H.247, G.249 No protein-ligand interaction detected (PLIP) GOL.23: 3 residues within 4Å: Chain A: I.129, G.132, T.134 4 PLIP interactions: 4 interactions with chain A Water bridges: A:G.132, A:T.134, A:T.134, A:T.134 GOL.43: 2 residues within 4Å: Chain B: R.269, H.270 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.269, B:R.269 Water bridges: B:D.268 GOL.44: 9 residues within 4Å: Chain B: G.53, F.54, R.57, Y.58, Q.146, Q.149, D.150, P.203, Y.215 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.57, B:Q.146, B:Y.215 Water bridges: B:D.150 GOL.45: 2 residues within 4Å: Chain B: H.247, G.249 No protein-ligand interaction detected (PLIP) GOL.46: 3 residues within 4Å: Chain B: I.129, G.132, T.134 2 PLIP interactions: 2 interactions with chain B Water bridges: B:G.132, B:T.134

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Besle, A. et al., A Micromolar O-Sulfated Thiohydroximate Inhibitor Bound to Plant Myrosinase. Acta Crystallogr.,Sect.F (2010)

Release Date

2010-02-09

Peptides

MYROSINASE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
M

B
M

MYROSINASE

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