SMTL ID : 1lk9.1

The Three-dimensional Structure of Alliinase from Garlic

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.53 Å

Oligo State

homo-dimer

Ligands

1 x NAG- NAG- BMA- FUC: 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-FUC.1: 5 residues within 4Å: Chain A: N.146, T.148, A.149, N.276 Chain B: Y.174 1 PLIP interactions: 1 interactions with chain A Water bridges: A:N.276

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.2: 3 residues within 4Å: Chain A: N.328, Q.408, F.411 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 5 residues within 4Å: Chain B: E.324, N.328, Q.408, F.411, D.412 No protein-ligand interaction detected (PLIP)

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

NAG-FUC.3: 7 residues within 4Å: Chain A: E.170, Y.174 Chain B: N.146, T.148, A.149, N.276, K.280 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.276, B:N.276, B:K.280, B:K.280, B:T.148, B:A.149

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

SO4.5: 2 residues within 4Å: Chain A: K.237, E.348 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.348 Salt bridges: A:K.237 SO4.6: 1 residues within 4Å: Chain A: R.323 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.323 SO4.7: 4 residues within 4Å: Chain A: A.120, A.121, K.122, K.239 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:K.122 Water bridges: A:A.121, A:A.121, A:A.121, A:D.123 Salt bridges: A:K.239 SO4.8: 2 residues within 4Å: Chain A: T.310, M.311 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:M.311 Water bridges: A:R.312, A:R.312 SO4.9: 4 residues within 4Å: Chain A: E.71, K.321, T.407, Q.408 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:E.71, A:R.325, A:Q.408 Water bridges: A:E.70, A:K.321, A:K.321, A:T.407, A:D.409 Salt bridges: A:K.321 SO4.10: 2 residues within 4Å: Chain A: R.355, M.356 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:M.356 SO4.15: 5 residues within 4Å: Chain B: K.74, Q.75, H.76, K.77, E.78 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:K.74, B:K.77, B:E.78 Water bridges: B:A.79 Salt bridges: B:K.77 SO4.16: 4 residues within 4Å: Chain B: E.369, W.370, E.371, R.426 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:E.369, B:E.371 Water bridges: B:E.372, B:R.426, B:R.426 Salt bridges: B:R.426 SO4.17: 2 residues within 4Å: Chain B: H.161, A.187 3 PLIP interactions: 3 interactions with chain B Water bridges: B:H.161, B:A.187 Salt bridges: B:H.161 SO4.18: 5 residues within 4Å: Chain B: E.114, A.120, A.121, K.122, K.239 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:E.114, B:A.121, B:K.122 Water bridges: B:E.114, B:E.114 Salt bridges: B:K.239 SO4.19: 2 residues within 4Å: Chain B: K.367, Y.399 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:S.396, B:Y.399 Water bridges: B:K.367, B:K.367 Salt bridges: B:K.367

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

CL.11: 6 residues within 4Å: Chain A: F.93, F.94, V.97, S.98, N.99, F.100 Ligand excluded by PLIP CL.20: 6 residues within 4Å: Chain B: F.93, F.94, V.97, S.98, N.99, F.100 Ligand excluded by PLIP

2 x PLP: PYRIDOXAL-5'-PHOSPHATE(Covalent)

PLP.12: 14 residues within 4Å: Chain A: 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 Chain B: Y.92 13 PLIP interactions: 12 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:Y.165, A:T.203, A:K.251 Hydrogen bonds: A:V.132, A:T.133, A:N.207, A:T.248, A:S.250, A:S.250, B:Y.92 Salt bridges: A:K.251, A:R.259 pi-Stacking: A:Y.165 PLP.21: 15 residues within 4Å: Chain A: Y.92 Chain B: 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 Ligands: DHA.22 14 PLIP interactions: 13 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:Y.165, B:T.203, B:V.227, B:K.251 Hydrogen bonds: B:V.132, B:T.133, B:T.133, B:N.207, B:Y.228, B:S.250, B:S.250, A:Y.92 Salt bridges: B:R.259 pi-Stacking: B:Y.165

2 x EPE: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID(Non-functional Binders)

EPE.13: 11 residues within 4Å: Chain A: Y.92, T.279, E.283 Chain B: S.63, G.64, Y.165, V.167, E.170, Q.388, R.401 Ligands: DHA.22 10 PLIP interactions: 8 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:S.63, B:G.64, B:E.170, B:Y.363, B:Q.388 Water bridges: B:R.401, B:R.401 Salt bridges: B:R.401, A:E.283, A:E.283 EPE.14: 12 residues within 4Å: Chain A: S.63, G.64, Y.165, V.167, E.170, Y.363, Q.388, R.401 Chain B: Y.92, F.93, T.279, E.283 13 PLIP interactions: 11 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:G.64, A:E.170, A:Y.363, A:Y.363, A:Q.388 Water bridges: A:E.170, A:N.207, A:R.401, A:R.401, A:R.401 Salt bridges: A:R.401, B:E.283, B:E.283

1 x DHA: 2-AMINO-ACRYLIC ACID(Non-covalent)

DHA.22: 11 residues within 4Å: Chain A: Y.92 Chain B: G.64, Y.165, N.207, Y.228, K.251, Y.363, Q.388, R.401 Ligands: EPE.13, PLP.21 10 PLIP interactions: 1 interactions with chain A, 9 interactions with chain B Hydrophobic interactions: A:Y.92 Hydrogen bonds: B:G.64, B:N.207, B:Y.228, B:Y.228, B:Q.388 Water bridges: B:R.401, B:R.401 Salt bridges: B:K.251, B:R.401

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kuettner, E.B. et al., The active principle of garlic at atomic resolution. J.Biol.Chem. (2002)

Release Date

2002-12-11

Peptides

ALLIIN LYASE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

ALLIIN LYASE