SMTL ID : 2hor.1

Crystal structure of alliinase from garlic- apo form

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-dimer

Ligands

2 x NAG- NAG- BMA- MAN- MAN- FUC: alpha-D-mannopyranose-(2-3)-[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-MAN-MAN-FUC.1: 10 residues within 4Å: Chain A: N.146, T.148, A.149, N.276, K.280 Chain B: E.170, K.173, Y.174, V.391 Ligands: SO4.6 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:N.276, A:K.280, A:K.280, B:V.391, B:K.173, B:K.173 Hydrophobic interactions: B:K.173, A:T.148 Water bridges: B:E.394 NAG-NAG-BMA-MAN-MAN-FUC.12: 10 residues within 4Å: Chain A: E.170, K.173, Y.174, V.391 Chain B: N.146, T.148, A.149, N.276, K.280 Ligands: SO4.17 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:N.276, B:K.280, B:K.280, A:V.391, A:K.173, A:K.173 Hydrophobic interactions: A:K.173, B:T.148

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

NAG.2: 3 residues within 4Å: Chain A: N.328, Q.408, F.411 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.13: 3 residues within 4Å: Chain B: N.328, Q.408, F.411 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.328, B:Q.408 Water bridges: B:E.324

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

SO4.3: 9 residues within 4Å: Chain A: S.63, G.64, Y.165, N.207, Y.228, K.251, Y.363, Q.388, R.401 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:G.64, A:Y.165, A:Y.165, A:N.207, A:Y.228, A:Y.363, A:Q.388 Water bridges: A:K.251, A:R.401, A:R.401 Salt bridges: A:K.251, A:R.401 SO4.4: 7 residues within 4Å: Chain A: G.131, V.132, T.133, T.248, S.250, R.259 Chain B: Y.92 12 PLIP interactions: 11 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:V.132, A:T.133, A:T.248, A:S.250, A:S.250, B:Y.92 Water bridges: A:T.133, A:T.133, A:T.133, A:K.251, A:K.251 Salt bridges: A:R.259 SO4.6: 2 residues within 4Å: Ligands: NAG-NAG-BMA-MAN-MAN-FUC.1, NAG-NAG-BMA-MAN-MAN-FUC.1 No protein-ligand interaction detected (PLIP) SO4.7: 5 residues within 4Å: Chain A: E.22, N.42, T.407, Q.408, D.409 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.42, A:Q.408, A:D.409 SO4.8: 5 residues within 4Å: Chain A: K.74, Q.75, H.76, K.77, E.78 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.77, A:E.78 Water bridges: A:A.79 Salt bridges: A:K.77 SO4.14: 9 residues within 4Å: Chain B: S.63, G.64, Y.165, N.207, Y.228, K.251, Y.363, Q.388, R.401 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:G.64, B:Y.165, B:N.207, B:Y.228, B:Q.388 Water bridges: B:K.251, B:R.401, B:R.401 Salt bridges: B:K.251, B:R.401 SO4.15: 7 residues within 4Å: Chain A: Y.92 Chain B: G.131, V.132, T.133, T.248, S.250, R.259 12 PLIP interactions: 11 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:V.132, B:T.133, B:T.133, B:S.250, B:S.250 Water bridges: B:T.133, B:K.251, B:K.251, B:R.259, B:R.259, A:Y.92 Salt bridges: B:R.259 SO4.17: 2 residues within 4Å: Ligands: NAG-NAG-BMA-MAN-MAN-FUC.12, NAG-NAG-BMA-MAN-MAN-FUC.12 No protein-ligand interaction detected (PLIP) SO4.18: 5 residues within 4Å: Chain B: E.22, N.42, T.407, Q.408, D.409 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.42, B:Q.408, B:D.409 SO4.19: 5 residues within 4Å: Chain B: K.74, Q.75, H.76, K.77, E.78 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:K.77, B:E.78 Water bridges: B:A.79 Salt bridges: B:K.77

2 x ACT: ACETATE ION(Non-functional Binders)

ACT.5: 5 residues within 4Å: Chain A: V.132, Y.165, T.203, D.225, V.227 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:Y.165, A:T.203, A:V.227 Hydrogen bonds: A:D.225 Water bridges: A:Y.165 ACT.16: 5 residues within 4Å: Chain B: V.132, Y.165, T.203, D.225, V.227 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:Y.165, B:T.203, B:V.227 Hydrogen bonds: B:D.225 Water bridges: B:Y.165, B:K.251

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

CL.9: 6 residues within 4Å: Chain A: F.93, F.94, V.97, S.98, N.99, F.100 Ligand excluded by PLIP CL.10: 4 residues within 4Å: Chain A: A.120, A.121, K.122, K.239 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 CL.21: 4 residues within 4Å: Chain B: A.120, A.121, K.122, K.239 Ligand excluded by PLIP

2 x NO3: NITRATE ION(Non-functional Binders)

NO3.11: 7 residues within 4Å: Chain A: H.137, F.175, K.177 Chain B: H.137, F.175, K.177 Ligands: NO3.22 No protein-ligand interaction detected (PLIP) NO3.22: 7 residues within 4Å: Chain A: H.137, F.175, K.177 Chain B: H.137, F.175, K.177 Ligands: NO3.11 No protein-ligand interaction detected (PLIP)

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
A

Alliin lyase 1

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