SMTL ID : 3lrl.1

Structure of alfa-galactosidase (MEL1) from Saccharomyces cerevisiae with melibiose

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-tetramer

Ligands

4 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.1: 5 residues within 4Å: Chain A: G.269, N.270, N.298 Chain D: N.381, L.382 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.298, A:N.298 Water bridges: A:N.298 NAG-NAG.9: 5 residues within 4Å: Chain B: G.269, N.270, N.298 Chain C: N.381, L.382 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.298, B:N.298 Water bridges: B:N.298 NAG-NAG.17: 5 residues within 4Å: Chain A: N.381, L.382 Chain C: G.269, N.270, N.298 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:N.298, C:N.298 Water bridges: C:N.298 NAG-NAG.25: 5 residues within 4Å: Chain B: N.381, L.382 Chain D: G.269, N.270, N.298 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:N.298, D:N.298 Water bridges: D:N.298

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.2: 6 residues within 4Å: Chain A: D.63, S.107, T.417, N.422, T.424, E.425 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:T.424 Hydrogen bonds: A:S.107 NAG-NAG.10: 6 residues within 4Å: Chain B: D.63, S.107, T.417, N.422, T.424, E.425 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:T.424 Hydrogen bonds: B:S.107 NAG-NAG.18: 6 residues within 4Å: Chain C: D.63, S.107, T.417, N.422, T.424, E.425 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:T.424 Hydrogen bonds: C:S.107 NAG-NAG.26: 6 residues within 4Å: Chain D: D.63, S.107, T.417, N.422, T.424, E.425 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:T.424 Hydrogen bonds: D:S.107

4 x GLC- GLA: alpha-D-galactopyranose-(1-6)-alpha-D-glucopyranose(Post Translational Modification)

GLC-GLA.3: 13 residues within 4Å: Chain A: D.72, D.73, Y.113, C.121, K.147, D.149, C.186, W.188, R.205, D.209, G.234, F.235 Chain D: Q.251 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain D Hydrogen bonds: A:D.73, A:Y.113, A:K.147, A:K.147, A:R.205, A:R.205, D:Q.251, A:G.234 Water bridges: A:K.147, A:R.205, D:V.19 GLC-GLA.11: 13 residues within 4Å: Chain B: D.72, D.73, Y.113, C.121, K.147, D.149, C.186, W.188, R.205, D.209, G.234, F.235 Chain C: Q.251 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain C Hydrogen bonds: B:D.73, B:Y.113, B:K.147, B:K.147, B:R.205, B:R.205, C:Q.251, B:G.234 Water bridges: B:K.147, B:R.205, C:V.19 GLC-GLA.19: 13 residues within 4Å: Chain A: Q.251 Chain C: D.72, D.73, Y.113, C.121, K.147, D.149, C.186, W.188, R.205, D.209, G.234, F.235 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain A Hydrogen bonds: C:D.73, C:Y.113, C:K.147, C:K.147, C:R.205, C:R.205, A:Q.251, C:G.234 Water bridges: C:K.147, C:R.205, A:V.19 GLC-GLA.27: 13 residues within 4Å: Chain B: Q.251 Chain D: D.72, D.73, Y.113, C.121, K.147, D.149, C.186, W.188, R.205, D.209, G.234, F.235 3 PLIP interactions: 1 interactions with chain D, 2 interactions with chain B Hydrogen bonds: D:D.73, D:Y.113, D:K.147, D:K.147, D:R.205, D:R.205, D:G.234, B:Q.251 Water bridges: D:K.147, D:R.205, B:V.19

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

NAG.4: 4 residues within 4Å: Chain A: H.98, D.101, H.102, N.105 Ligand excluded by PLIP NAG.5: 4 residues within 4Å: Chain A: N.175, G.178, R.179, P.180 Ligand excluded by PLIP NAG.6: 3 residues within 4Å: Chain A: D.273, S.302, N.403 Ligand excluded by PLIP NAG.7: 4 residues within 4Å: Chain A: W.328, Y.330, I.343, N.370 Ligand excluded by PLIP NAG.12: 4 residues within 4Å: Chain B: H.98, D.101, H.102, N.105 Ligand excluded by PLIP NAG.13: 4 residues within 4Å: Chain B: N.175, G.178, R.179, P.180 Ligand excluded by PLIP NAG.14: 3 residues within 4Å: Chain B: D.273, S.302, N.403 Ligand excluded by PLIP NAG.15: 4 residues within 4Å: Chain B: W.328, Y.330, I.343, N.370 Ligand excluded by PLIP NAG.20: 4 residues within 4Å: Chain C: H.98, D.101, H.102, N.105 Ligand excluded by PLIP NAG.21: 4 residues within 4Å: Chain C: N.175, G.178, R.179, P.180 Ligand excluded by PLIP NAG.22: 3 residues within 4Å: Chain C: D.273, S.302, N.403 Ligand excluded by PLIP NAG.23: 4 residues within 4Å: Chain C: W.328, Y.330, I.343, N.370 Ligand excluded by PLIP NAG.28: 4 residues within 4Å: Chain D: H.98, D.101, H.102, N.105 Ligand excluded by PLIP NAG.29: 4 residues within 4Å: Chain D: N.175, G.178, R.179, P.180 Ligand excluded by PLIP NAG.30: 3 residues within 4Å: Chain D: D.273, S.302, N.403 Ligand excluded by PLIP NAG.31: 4 residues within 4Å: Chain D: W.328, Y.330, I.343, N.370 Ligand excluded by PLIP

4 x NA: SODIUM ION(Non-functional Binders)

NA.8: 2 residues within 4Å: Chain A: H.98, H.102 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.98 NA.16: 2 residues within 4Å: Chain B: H.98, H.102 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:H.98 NA.24: 2 residues within 4Å: Chain C: H.98, H.102 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:H.98 NA.32: 2 residues within 4Å: Chain D: H.98, H.102 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:H.98

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fernandez-Leiro, R. et al., Structural analysis of Saccharomyces cerevisiae alpha-galactosidase and its complexes with natural substrates reveals new insights into substrate specificity of GH27 glycosidases. J.Biol.Chem. (2010)

Release Date

2010-06-30

Peptides

Alpha-galactosidase 1: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

Alpha-galactosidase 1

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