SMTL ID : 2hox.1 (2 other biounits)

alliinase from allium sativum (garlic)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.40 Å

Oligo State

homo-dimer

Ligands

1 x NAG- NAG- BMA- XYP- BMA- FUC: beta-D-xylopyranose-(1-2)-[beta-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-BMA-FUC.1: 5 residues within 4Å: Chain A: N.146, T.148, A.149, N.276 Chain B: Y.174 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain B Water bridges: A:N.276, A:N.276, A:K.280, A:K.280, A:K.280, B:E.170, B:K.173

1 x NAG- FUC: alpha-L-fucopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-FUC.2: 4 residues within 4Å: Chain A: Y.174 Chain B: N.146, T.148, A.149 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:Y.174 Hydrogen bonds: B:N.146, B:T.148 Water bridges: B:A.149

6 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)(Non-functional Binders)(Non-covalent)

NAG.3: 5 residues within 4Å: Chain A: N.328, Q.408, F.411, D.412 Ligands: NAG.4 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.328, A:Q.408 Water bridges: A:E.324, A:D.412 NAG.4: 1 residues within 4Å: Ligands: NAG.3 No protein-ligand interaction detected (PLIP) NAG.5: 2 residues within 4Å: Chain A: N.191, K.218 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:K.218 Water bridges: A:N.191, A:N.191, A:N.191 NAG.8: 6 residues within 4Å: Chain B: E.324, R.325, N.328, Q.408, F.411 Ligands: NAG.9 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:E.324, B:R.325 Hydrogen bonds: B:E.324, B:N.328 Water bridges: B:E.324, B:E.324, B:E.324 NAG.9: 1 residues within 4Å: Ligands: NAG.8 No protein-ligand interaction detected (PLIP) NAG.10: 1 residues within 4Å: Chain B: N.191 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.191 Water bridges: B:N.191

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.6: 6 residues within 4Å: Chain A: F.93, F.94, V.97, S.98, N.99, F.100 Ligand excluded by PLIP CL.11: 6 residues within 4Å: Chain B: F.93, F.94, V.97, S.98, N.99, F.100 Ligand excluded by PLIP

2 x P1T: 2-[({3-HYDROXY-2-METHYL-5-[(PHOSPHONOOXY)METHYL]PYRIDIN-4-YL}METHYL)AMINO]ACRYLIC ACID(Non-covalent)

P1T.7: 18 residues within 4Å: Chain A: G.64, G.131, V.132, T.133, Y.165, T.203, N.207, D.225, V.227, Y.228, T.248, S.250, K.251, R.259, Y.363, Q.388, R.401 Chain B: Y.92 19 PLIP interactions: 18 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:Y.165, A:T.203, A:Y.228, B:Y.92 Hydrogen bonds: A:G.64, A:V.132, A:T.133, A:N.207, A:T.248, A:S.250, A:K.251, A:Y.363, A:Q.388 Water bridges: A:R.401, A:R.401 Salt bridges: A:K.251, A:R.259, A:R.401 pi-Stacking: A:Y.165 P1T.12: 19 residues within 4Å: Chain A: Y.92 Chain B: S.63, G.64, G.131, V.132, T.133, Y.165, T.203, N.207, D.225, V.227, Y.228, T.248, S.250, K.251, R.259, Y.363, Q.388, R.401 20 PLIP interactions: 18 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:Y.165, B:T.203, B:V.227, A:Y.92 Hydrogen bonds: B:G.64, B:V.132, B:T.133, B:T.133, B:N.207, B:Y.228, B:S.250, B:K.251, B:Q.388, A:Y.92 Water bridges: B:R.401, B:R.401 Salt bridges: B:K.251, B:R.259, B:R.401 pi-Stacking: B:Y.165

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Shimon, L.J. et al., Two Structures of Alliinase from Alliium sativum L.: Apo Form and Ternary Complex with Aminoacrylate Reaction Intermediate Covalently Bound to the PLP Cofactor. J.Mol.Biol. (2007)

Release Date

2007-02-06

Peptides

Alliin lyase 1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Alliin lyase 1

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