SMTL ID : 1e73.1

2-F-glucosylated MYROSINASE FROM SINAPIS ALBA with bound L-ascorbate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

homo-dimer

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: 6 residues within 4Å: Chain A: S.207, N.218, T.221, E.305, R.306, T.345 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:R.306 NAG-NAG.25: 6 residues within 4Å: Chain B: S.207, N.218, T.221, E.305, R.306, T.345 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:R.306

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.2: 4 residues within 4Å: Chain A: N.265, T.267, D.268, A.362 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-XYP-FUC.26: 4 residues within 4Å: Chain B: N.265, T.267, D.268, A.362 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.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 NAG-NAG-BMA-XYP-MAN-MAN-FUC.27: 4 residues within 4Å: Chain B: N.292, T.294, Q.297, I.300 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.297, B:Q.297, B:Q.297

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

NAG.4: 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.5: 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.6: 4 residues within 4Å: Chain A: K.165, D.239, L.240, N.244 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.240 Water bridges: A:K.243, A:N.244 NAG.7: 3 residues within 4Å: Chain A: Y.58, N.60 Ligands: SO4.18 1 PLIP interactions: 1 interactions with chain A Water bridges: A:S.213 NAG.8: 3 residues within 4Å: Chain A: S.344, N.346, M.351 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.344 Water bridges: A:N.346, A:N.346, A:N.346 NAG.9: 2 residues within 4Å: Chain A: N.482, 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.28: 6 residues within 4Å: Chain B: T.17, D.18, A.19, N.21, S.24, P.501 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:P.501 Hydrogen bonds: B:N.21 Water bridges: B:A.19, B:P.501 NAG.29: 2 residues within 4Å: Chain B: N.90, S.500 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.90, B:S.500 NAG.30: 4 residues within 4Å: Chain B: K.165, D.239, L.240, N.244 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:L.240 Water bridges: B:K.243, B:N.244 NAG.31: 3 residues within 4Å: Chain B: Y.58, N.60 Ligands: SO4.42 1 PLIP interactions: 1 interactions with chain B Water bridges: B:S.213 NAG.32: 3 residues within 4Å: Chain B: S.344, N.346, M.351 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.344 Water bridges: B:N.346, B:N.346, B:N.346 NAG.33: 2 residues within 4Å: Chain B: N.482, D.485 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.482, B:D.485 Water bridges: B:T.484, B:D.485

2 x ASC: ASCORBIC ACID(Non-covalent)

ASC.10: 9 residues within 4Å: Chain A: Q.187, I.257, R.259, Y.330, F.331, F.371, F.473 Ligands: G2F.11, SO4.19 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.187, A:R.259, A:R.259 Water bridges: A:S.190 Salt bridges: A:R.259 ASC.34: 9 residues within 4Å: Chain B: Q.187, I.257, R.259, Y.330, F.331, F.371, F.473 Ligands: G2F.35, SO4.43 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:Q.187, B:R.259, B:R.259 Water bridges: B:S.190, B:E.464 Salt bridges: B:R.259

2 x G2F: 2-deoxy-2-fluoro-alpha-D-glucopyranose(Post Translational Modification)

G2F.11: 11 residues within 4Å: Chain A: Q.39, H.141, N.186, Q.187, Y.330, E.409, W.457, E.464, F.465, F.473 Ligands: ASC.10 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Q.39, A:Q.39, A:H.141, A:Y.330 Water bridges: A:N.462 Halogen bonds: A:N.186 G2F.35: 11 residues within 4Å: Chain B: Q.39, H.141, N.186, Q.187, Y.330, E.409, W.457, E.464, F.465, F.473 Ligands: ASC.34 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:Q.39, B:Q.39, B:H.141 Water bridges: B:N.462, B:E.464 Halogen bonds: B:N.186

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

SO4.12: 3 residues within 4Å: Chain A: E.153, R.205 Chain B: R.106 Ligand excluded by PLIP SO4.13: 2 residues within 4Å: Chain A: K.108, R.111 Ligand excluded by PLIP SO4.14: 4 residues within 4Å: Chain A: R.259, Q.333, L.357 Ligands: SO4.19 Ligand excluded by PLIP SO4.15: 3 residues within 4Å: Chain A: Q.7, E.8, N.9 Ligand excluded by PLIP SO4.16: 4 residues within 4Å: Chain A: R.269, H.270, A.273, R.277 Ligand excluded by PLIP SO4.17: 3 residues within 4Å: Chain A: R.109, V.113, E.173 Ligand excluded by PLIP SO4.18: 3 residues within 4Å: Chain A: N.60, H.66 Ligands: NAG.7 Ligand excluded by PLIP SO4.19: 4 residues within 4Å: Chain A: R.194, R.259 Ligands: ASC.10, SO4.14 Ligand excluded by PLIP SO4.36: 3 residues within 4Å: Chain A: R.106 Chain B: E.153, R.205 Ligand excluded by PLIP SO4.37: 2 residues within 4Å: Chain B: K.108, R.111 Ligand excluded by PLIP SO4.38: 4 residues within 4Å: Chain B: R.259, Q.333, L.357 Ligands: SO4.43 Ligand excluded by PLIP SO4.39: 3 residues within 4Å: Chain B: Q.7, E.8, N.9 Ligand excluded by PLIP SO4.40: 4 residues within 4Å: Chain B: R.269, H.270, A.273, R.277 Ligand excluded by PLIP SO4.41: 3 residues within 4Å: Chain B: R.109, V.113, E.173 Ligand excluded by PLIP SO4.42: 3 residues within 4Å: Chain B: N.60, H.66 Ligands: NAG.31 Ligand excluded by PLIP SO4.43: 4 residues within 4Å: Chain B: R.194, R.259 Ligands: ASC.34, SO4.38 Ligand excluded by PLIP

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.20: 1 residues within 4Å: Chain A: R.269 No protein-ligand interaction detected (PLIP) GOL.21: 8 residues within 4Å: Chain A: F.54, R.57, Y.58, 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.22: 3 residues within 4Å: Chain A: H.247, Q.248, G.249 2 PLIP interactions: 2 interactions with chain A Water bridges: A:K.180, A:T.246 GOL.23: 3 residues within 4Å: Chain A: I.129, G.132, T.134 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:I.129, A:T.134 Water bridges: A:T.134, A:T.134 GOL.44: 1 residues within 4Å: Chain B: R.269 No protein-ligand interaction detected (PLIP) GOL.45: 8 residues within 4Å: Chain B: F.54, R.57, Y.58, Q.146, Q.149, D.150, P.203, Y.215 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.57, B:Q.146 Water bridges: B:D.150 GOL.46: 3 residues within 4Å: Chain B: H.247, Q.248, G.249 2 PLIP interactions: 2 interactions with chain B Water bridges: B:K.180, B:T.246 GOL.47: 3 residues within 4Å: Chain B: I.129, G.132, T.134 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:I.129, B:T.134 Water bridges: B:T.134

2 x ZN: ZINC ION(Non-covalent)

ZN.24: 5 residues within 4Å: Chain A: H.56, D.70 Chain B: H.56, D.70 Ligands: ZN.48 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain A Metal complexes: B:H.56, B:D.70, A:H.56, A:D.70, A:D.70 ZN.48: 5 residues within 4Å: Chain A: H.56, D.70 Chain B: H.56, D.70 Ligands: ZN.24 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

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Burmeister, W.P. et al., High Resolution X-Ray Crystallography Shows that Ascorbate is a Cofactor for Myrosinase and Substitutes for the Function of the Catalytic Base. J.Biol.Chem. (2000)

Release Date

2001-01-05

Peptides

MYROSINASE MA1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
M

B
M

MYROSINASE MA1

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