SMTL ID : 1myr.1

MYROSINASE FROM SINAPIS ALBA

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.64 Å

Oligo State

homo-dimer

Ligands

4 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, R.306, T.345 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:R.306 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) NAG-NAG.25: 5 residues within 4Å: Chain B: S.207, N.218, T.221, R.306, T.345 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:R.306 NAG-NAG.28: 7 residues within 4Å: Chain B: Y.264, N.265, D.266, N.361, A.362, S.363, H.365 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(Post Translational Modification)

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- 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(Post Translational Modification)

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.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 Water bridges: B:Q.297

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

NAG.5: 6 residues within 4Å: Chain A: T.17, D.18, G.19, N.21, S.24, P.501 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:P.501 Hydrogen bonds: A:N.21 Water bridges: A:D.18, A:G.19, A:S.23, A:N.441 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 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.240 Hydrogen bonds: A:N.244 Water bridges: A:K.165, A:K.243, A:N.244 NAG.8: 1 residues within 4Å: Chain A: N.346 No protein-ligand interaction detected (PLIP) NAG.9: 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.29: 6 residues within 4Å: Chain B: T.17, D.18, G.19, N.21, S.24, P.501 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:P.501 Hydrogen bonds: B:N.21 Water bridges: B:G.19, B:S.23, B:N.441, B:P.501 NAG.30: 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.31: 4 residues within 4Å: Chain B: K.165, D.239, L.240, N.244 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:L.240 Hydrogen bonds: B:N.244 Water bridges: B:K.165, B:K.243, B:N.244 NAG.32: 1 residues within 4Å: Chain B: N.346 No protein-ligand interaction detected (PLIP) NAG.33: 3 residues within 4Å: Chain B: N.482, T.484, 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 ZN: ZINC ION(Non-covalent)

ZN.10: 5 residues within 4Å: Chain A: H.56, D.70 Chain B: H.56, D.70 Ligands: ZN.34 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 ZN.34: 5 residues within 4Å: Chain A: H.56, D.70 Chain B: H.56, D.70 Ligands: ZN.10 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

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

SO4.11: 3 residues within 4Å: Chain A: E.153, R.205 Chain B: R.106 Ligand excluded by PLIP SO4.12: 2 residues within 4Å: Chain A: K.108, R.111 Ligand excluded by PLIP SO4.13: 4 residues within 4Å: Chain A: R.259, Q.333, L.357 Ligands: SO4.18 Ligand excluded by PLIP SO4.14: 3 residues within 4Å: Chain A: Q.7, E.8, N.9 Ligand excluded by PLIP SO4.15: 4 residues within 4Å: Chain A: R.269, H.270, A.273, R.277 Ligand excluded by PLIP SO4.16: 4 residues within 4Å: Chain A: R.109, V.113, L.170, E.173 Ligand excluded by PLIP SO4.17: 2 residues within 4Å: Chain A: D.60, H.66 Ligand excluded by PLIP SO4.18: 4 residues within 4Å: Chain A: R.194, L.200, R.259 Ligands: SO4.13 Ligand excluded by PLIP SO4.19: 1 residues within 4Å: Chain A: R.269 Ligand excluded by PLIP SO4.20: 2 residues within 4Å: Chain A: Y.427, K.490 Ligand excluded by PLIP SO4.35: 3 residues within 4Å: Chain A: R.106 Chain B: E.153, R.205 Ligand excluded by PLIP SO4.36: 2 residues within 4Å: Chain B: K.108, R.111 Ligand excluded by PLIP SO4.37: 4 residues within 4Å: Chain B: R.259, Q.333, L.357 Ligands: SO4.42 Ligand excluded by PLIP SO4.38: 3 residues within 4Å: Chain B: Q.7, E.8, N.9 Ligand excluded by PLIP SO4.39: 4 residues within 4Å: Chain B: R.269, H.270, A.273, R.277 Ligand excluded by PLIP SO4.40: 4 residues within 4Å: Chain B: R.109, V.113, L.170, E.173 Ligand excluded by PLIP SO4.41: 2 residues within 4Å: Chain B: D.60, H.66 Ligand excluded by PLIP SO4.42: 4 residues within 4Å: Chain B: R.194, L.200, R.259 Ligands: SO4.37 Ligand excluded by PLIP SO4.43: 1 residues within 4Å: Chain B: R.269 Ligand excluded by PLIP SO4.44: 2 residues within 4Å: Chain B: Y.427, K.490 Ligand excluded by PLIP

8 x GOL: GLYCEROL(Non-functional Binders)

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 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: 9 residues within 4Å: Chain A: Q.39, H.141, N.186, Q.187, N.328, E.409, W.457, E.464, F.465 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:Q.39, A:Q.39, A:N.186, A:Q.187, A:N.328, A:E.464 Water bridges: A:N.462 GOL.24: 4 residues within 4Å: Chain A: I.129, G.132, I.133, T.134 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:I.129 Water bridges: A:G.132, A:T.134, A:T.134 GOL.45: 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.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: 9 residues within 4Å: Chain B: Q.39, H.141, N.186, Q.187, N.328, E.409, W.457, E.464, F.465 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:Q.39, B:Q.39, B:N.186, B:Q.187, B:N.328, B:E.464 Water bridges: B:N.462 GOL.48: 4 residues within 4Å: Chain B: I.129, G.132, I.133, T.134 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:I.129 Water bridges: B:G.132, B:T.134

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Burmeister, W.P. et al., The crystal structures of Sinapis alba myrosinase and a covalent glycosyl-enzyme intermediate provide insights into the substrate recognition and active-site machinery of an S-glycosidase. Structure (1997)

Release Date

1997-06-16

Peptides

MYROSINASE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

MYROSINASE