SMTL ID : 1e72.1

Myrosinase from Sinapis alba with bound gluco-hydroximolactam and sulfate or ascorbate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 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: 5 residues within 4Å: Chain A: N.265, T.267, D.268, A.362, S.363 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, S.363 No protein-ligand interaction detected (PLIP)

2 x NAG- NAG- BMA- XYP- MAN- FUC: beta-D-xylopyranose-(1-2)-[alpha-D-mannopyranose-(1-3)]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-FUC.3: 4 residues within 4Å: Chain A: N.292, T.294, Q.297, I.300 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.297, A:Q.297, A:Q.297, A:Q.297, A:Q.297 Water bridges: A:Q.297, A:D.301 NAG-NAG-BMA-XYP-MAN-FUC.27: 4 residues within 4Å: Chain B: N.292, T.294, Q.297, I.300 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.297, B:Q.297, B:Q.297, B:Q.297, B:Q.297 Water bridges: 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 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:P.501 Hydrogen bonds: A:D.18, A:N.21 Water bridges: A:A.19, A:N.441 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: 3 residues within 4Å: Chain A: K.165, L.240, N.244 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.240 Hydrogen bonds: A:N.244 Water bridges: A:N.244 NAG.7: 4 residues within 4Å: Chain A: Y.58, N.60, S.213 Ligands: SO4.19 2 PLIP interactions: 2 interactions with chain A Water bridges: A:N.60, A:S.213 NAG.8: 3 residues within 4Å: Chain A: S.344, N.346, M.351 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.344 Water bridges: 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 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:P.501 Hydrogen bonds: B:N.21 Water bridges: B:A.19, B:N.441, 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: 3 residues within 4Å: Chain B: K.165, L.240, N.244 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:L.240 Hydrogen bonds: B:N.244 Water bridges: B:N.244 NAG.31: 4 residues within 4Å: Chain B: Y.58, N.60, S.213 Ligands: SO4.43 2 PLIP interactions: 2 interactions with chain B Water bridges: B:N.60, B:S.213 NAG.32: 3 residues within 4Å: Chain B: S.344, N.346, M.351 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.344 Water bridges: B:N.346, B:N.346 NAG.33: 2 residues within 4Å: Chain B: N.482, 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 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: GOX.11, SO4.23 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: GOX.35, SO4.47 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 GOX: (2S,3S,4R,5R)-6-(HYDROXYAMINO)-2-(HYDROXYMETHYL)-2,3,4,5-TETRAHYDROPYRIDINE-3,4,5-TRIOL(Non-covalent)

GOX.11: 14 residues within 4Å: Chain A: Q.39, H.141, N.186, Q.187, I.257, N.328, Y.330, E.409, W.457, E.464, F.465, F.473 Ligands: ASC.10, SO4.23 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:Q.39, A:Q.39, A:H.141, A:N.186, A:Q.187, A:Q.187, A:N.328 Water bridges: A:N.462, A:E.464 GOX.35: 14 residues within 4Å: Chain B: Q.39, H.141, N.186, Q.187, I.257, N.328, Y.330, E.409, W.457, E.464, F.465, F.473 Ligands: ASC.34, SO4.47 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:Q.39, B:Q.39, B:H.141, B:N.186, B:Q.187, B:Q.187, B:N.328 Water bridges: B:N.462, B:E.464, B:E.464, B:E.464

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.36 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 ZN.36: 5 residues within 4Å: Chain A: H.56, D.70 Chain B: H.56, D.70 Ligands: ZN.12 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

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

SO4.13: 3 residues within 4Å: Chain A: E.153, R.205 Chain B: R.106 Ligand excluded by PLIP SO4.14: 2 residues within 4Å: Chain A: K.108, R.111 Ligand excluded by PLIP SO4.15: 2 residues within 4Å: Chain A: R.259, Q.333 Ligand excluded by PLIP SO4.16: 3 residues within 4Å: Chain A: Q.7, E.8, N.9 Ligand excluded by PLIP SO4.17: 4 residues within 4Å: Chain A: R.269, H.270, A.273, R.277 Ligand excluded by PLIP SO4.18: 3 residues within 4Å: Chain A: R.109, V.113, E.173 Ligand excluded by PLIP SO4.19: 3 residues within 4Å: Chain A: N.60, H.66 Ligands: NAG.7 Ligand excluded by PLIP SO4.23: 6 residues within 4Å: Chain A: Q.187, I.257, R.259, Y.330 Ligands: ASC.10, GOX.11 Ligand excluded by PLIP SO4.37: 3 residues within 4Å: Chain A: R.106 Chain B: E.153, R.205 Ligand excluded by PLIP SO4.38: 2 residues within 4Å: Chain B: K.108, R.111 Ligand excluded by PLIP SO4.39: 2 residues within 4Å: Chain B: R.259, Q.333 Ligand excluded by PLIP SO4.40: 3 residues within 4Å: Chain B: Q.7, E.8, N.9 Ligand excluded by PLIP SO4.41: 4 residues within 4Å: Chain B: R.269, H.270, A.273, R.277 Ligand excluded by PLIP SO4.42: 3 residues within 4Å: Chain B: R.109, V.113, E.173 Ligand excluded by PLIP SO4.43: 3 residues within 4Å: Chain B: N.60, H.66 Ligands: NAG.31 Ligand excluded by PLIP SO4.47: 6 residues within 4Å: Chain B: Q.187, I.257, R.259, Y.330 Ligands: ASC.34, GOX.35 Ligand excluded by PLIP

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.20: 9 residues within 4Å: Chain A: G.53, 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.21: 3 residues within 4Å: Chain A: H.247, Q.248, G.249 No protein-ligand interaction detected (PLIP) GOL.22: 3 residues within 4Å: Chain A: I.129, G.132, T.134 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:I.129, A:T.134 Water bridges: A:G.132, A:T.134, A:T.134 GOL.24: 1 residues within 4Å: Chain A: R.269 No protein-ligand interaction detected (PLIP) 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 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.57, B:Q.146 Water bridges: B:D.150 GOL.45: 3 residues within 4Å: Chain B: H.247, Q.248, G.249 No protein-ligand interaction detected (PLIP) GOL.46: 3 residues within 4Å: Chain B: I.129, G.132, T.134 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:I.129, B:T.134 Water bridges: B:G.132, B:T.134 GOL.48: 1 residues within 4Å: Chain B: R.269 No protein-ligand interaction detected (PLIP)

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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