SMTL ID : 1e6q.1

MYROSINASE FROM SINAPIS ALBA with the bound transition state analogue gluco-tetrazole

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.35 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.23: 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: 6 residues within 4Å: Chain A: N.265, T.267, D.268, A.362, S.363 Ligands: GOL.22 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-XYP-FUC.24: 6 residues within 4Å: Chain B: N.265, T.267, D.268, A.362, S.363 Ligands: GOL.44 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 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.25: 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 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 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 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.240 Hydrogen bonds: A:N.244 Water bridges: A:K.243, A:N.244 NAG.7: 3 residues within 4Å: Chain A: Y.58, N.60 Ligands: SO4.20 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 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.26: 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.27: 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.28: 4 residues within 4Å: Chain B: K.165, D.239, L.240, N.244 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:L.240 Hydrogen bonds: B:N.244 Water bridges: B:K.243, B:N.244 NAG.29: 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.30: 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.31: 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 NTZ: NOJIRIMYCINE TETRAZOLE(Non-covalent)

NTZ.10: 10 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 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:Q.39, A:Q.39, A:H.141, A:N.186, A:Q.187, A:Q.187 Water bridges: A:N.462, A:E.464 NTZ.32: 10 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 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:Q.39, B:Q.39, B:H.141, B:N.186, B:Q.187, B:Q.187 Water bridges: B:N.462, B:E.464, B:E.464, B:E.464

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.11: 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.12: 2 residues within 4Å: Chain A: H.247, G.249 No protein-ligand interaction detected (PLIP) GOL.13: 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.22: 1 residues within 4Å: Ligands: NAG-NAG-BMA-XYP-FUC.2 No protein-ligand interaction detected (PLIP) GOL.33: 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.34: 2 residues within 4Å: Chain B: H.247, G.249 No protein-ligand interaction detected (PLIP) GOL.35: 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.44: 1 residues within 4Å: Ligands: NAG-NAG-BMA-XYP-FUC.24 No protein-ligand interaction detected (PLIP)

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

SO4.14: 3 residues within 4Å: Chain A: E.153, R.205 Chain B: R.106 9 PLIP interactions: 5 interactions with chain B, 4 interactions with chain A Water bridges: B:R.106, B:R.106, B:R.106, B:R.106, B:R.106, A:E.153, A:R.205, A:R.205 Salt bridges: A:R.205 SO4.15: 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 SO4.16: 2 residues within 4Å: Chain A: R.259, Q.333 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.333 Water bridges: A:R.194, A:R.259, A:R.259 Salt bridges: A:R.259 SO4.17: 3 residues within 4Å: Chain A: 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 SO4.18: 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 SO4.19: 3 residues within 4Å: Chain A: R.109, V.113, E.173 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.109 SO4.20: 3 residues within 4Å: Chain A: N.60, H.66 Ligands: NAG.7 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 A: R.106 Chain B: E.153, R.205 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain A Water bridges: B:R.205, B:R.205, B:R.205, B:E.222 Salt bridges: B:R.205 Hydrogen bonds: A:R.106 SO4.37: 2 residues within 4Å: Chain B: K.108, R.111 2 PLIP interactions: 2 interactions with chain B Water bridges: B:R.111 Salt bridges: B:R.111 SO4.38: 2 residues within 4Å: Chain B: R.259, Q.333 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:Q.333 Water bridges: B:Y.189, B:R.194, B:R.259, B:R.259 Salt bridges: B:R.259 SO4.39: 3 residues within 4Å: Chain B: Q.7, E.8, N.9 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.8, B:N.9, B:N.9 Water bridges: B:E.8 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: 3 residues within 4Å: Chain B: R.109, V.113, 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.29 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.60 Salt bridges: B:H.66

2 x ZN: ZINC ION(Non-covalent)

ZN.21: 5 residues within 4Å: Chain A: H.56, D.70 Chain B: H.56, D.70 Ligands: ZN.43 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.43: 5 residues within 4Å: Chain A: H.56, D.70 Chain B: H.56, D.70 Ligands: ZN.21 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Metal complexes: B:H.56, B:D.70, B:D.70, A:H.56, A: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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