SMTL ID : 3lrk.1

Structure of alfa-galactosidase (MEL1) from Saccharomyces cerevisiae

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.95 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: 6 residues within 4Å: Chain A: G.267, 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 Water bridges: A:N.298, A:N.298 NAG-NAG.12: 6 residues within 4Å: Chain B: G.267, 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 Water bridges: B:N.298, B:N.298 NAG-NAG.23: 6 residues within 4Å: Chain A: N.381, L.382 Chain C: G.267, G.269, N.270, N.298 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:N.298 Water bridges: C:N.298, C:N.298 NAG-NAG.34: 6 residues within 4Å: Chain B: N.381, L.382 Chain D: G.267, G.269, N.270, N.298 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:N.298 Water bridges: D:N.298, 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 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:T.424 Hydrogen bonds: A:S.107 Water bridges: A:N.105 NAG-NAG.13: 6 residues within 4Å: Chain B: D.63, S.107, T.417, N.422, T.424, E.425 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:T.424 Hydrogen bonds: B:S.107 Water bridges: B:N.105 NAG-NAG.24: 6 residues within 4Å: Chain C: D.63, S.107, T.417, N.422, T.424, E.425 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:T.424 Hydrogen bonds: C:S.107 Water bridges: C:N.105 NAG-NAG.35: 6 residues within 4Å: Chain D: D.63, S.107, T.417, N.422, T.424, E.425 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:T.424 Hydrogen bonds: D:S.107 Water bridges: D:N.105

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

NAG.3: 4 residues within 4Å: Chain A: H.98, H.102, N.105 Ligands: BTB.11 Ligand excluded by PLIP NAG.4: 4 residues within 4Å: Chain A: N.175, G.178, R.179, P.180 Ligand excluded by PLIP NAG.5: 4 residues within 4Å: Chain A: D.273, K.300, S.302, N.403 Ligand excluded by PLIP NAG.6: 3 residues within 4Å: Chain A: W.328, Y.330, N.370 Ligand excluded by PLIP NAG.14: 4 residues within 4Å: Chain B: H.98, H.102, N.105 Ligands: BTB.22 Ligand excluded by PLIP NAG.15: 4 residues within 4Å: Chain B: N.175, G.178, R.179, P.180 Ligand excluded by PLIP NAG.16: 4 residues within 4Å: Chain B: D.273, K.300, S.302, N.403 Ligand excluded by PLIP NAG.17: 3 residues within 4Å: Chain B: W.328, Y.330, N.370 Ligand excluded by PLIP NAG.25: 4 residues within 4Å: Chain C: H.98, H.102, N.105 Ligands: BTB.33 Ligand excluded by PLIP NAG.26: 4 residues within 4Å: Chain C: N.175, G.178, R.179, P.180 Ligand excluded by PLIP NAG.27: 4 residues within 4Å: Chain C: D.273, K.300, S.302, N.403 Ligand excluded by PLIP NAG.28: 3 residues within 4Å: Chain C: W.328, Y.330, N.370 Ligand excluded by PLIP NAG.36: 4 residues within 4Å: Chain D: H.98, H.102, N.105 Ligands: BTB.44 Ligand excluded by PLIP NAG.37: 4 residues within 4Å: Chain D: N.175, G.178, R.179, P.180 Ligand excluded by PLIP NAG.38: 4 residues within 4Å: Chain D: D.273, K.300, S.302, N.403 Ligand excluded by PLIP NAG.39: 3 residues within 4Å: Chain D: W.328, Y.330, N.370 Ligand excluded by PLIP

12 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 9 residues within 4Å: Chain A: W.37, D.72, D.73, Y.113, C.121, A.122, K.147, D.149 Ligands: GOL.8 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:A.122, A:K.147, A:K.147 Water bridges: A:C.121 GOL.8: 11 residues within 4Å: Chain A: D.35, W.37, N.38, D.72, K.147, R.205, D.209, V.210, D.262, N.263 Ligands: GOL.7 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:D.35, A:K.147, A:K.147, A:R.205, A:V.210, A:N.263 Water bridges: A:D.35, A:R.205, A:D.262, A:D.262 GOL.9: 9 residues within 4Å: Chain A: M.64, S.308, Q.309, A.310, N.399, V.401, I.419, L.420, Y.421 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:S.308, A:A.310, A:N.399, A:Y.421 Water bridges: A:S.311, A:V.401 GOL.18: 9 residues within 4Å: Chain B: W.37, D.72, D.73, Y.113, C.121, A.122, K.147, D.149 Ligands: GOL.19 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:A.122, B:K.147, B:K.147 Water bridges: B:C.121 GOL.19: 11 residues within 4Å: Chain B: D.35, W.37, N.38, D.72, K.147, R.205, D.209, V.210, D.262, N.263 Ligands: GOL.18 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:D.35, B:K.147, B:K.147, B:R.205, B:V.210, B:N.263 Water bridges: B:D.35, B:R.205, B:D.262, B:D.262 GOL.20: 9 residues within 4Å: Chain B: M.64, S.308, Q.309, A.310, N.399, V.401, I.419, L.420, Y.421 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:S.308, B:A.310, B:N.399, B:Y.421 Water bridges: B:S.311, B:V.401 GOL.29: 9 residues within 4Å: Chain C: W.37, D.72, D.73, Y.113, C.121, A.122, K.147, D.149 Ligands: GOL.30 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:A.122, C:K.147, C:K.147 Water bridges: C:C.121 GOL.30: 11 residues within 4Å: Chain C: D.35, W.37, N.38, D.72, K.147, R.205, D.209, V.210, D.262, N.263 Ligands: GOL.29 10 PLIP interactions: 10 interactions with chain C Hydrogen bonds: C:D.35, C:K.147, C:K.147, C:R.205, C:V.210, C:N.263 Water bridges: C:D.35, C:R.205, C:D.262, C:D.262 GOL.31: 9 residues within 4Å: Chain C: M.64, S.308, Q.309, A.310, N.399, V.401, I.419, L.420, Y.421 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:S.308, C:A.310, C:N.399, C:Y.421 Water bridges: C:S.311, C:V.401 GOL.40: 9 residues within 4Å: Chain D: W.37, D.72, D.73, Y.113, C.121, A.122, K.147, D.149 Ligands: GOL.41 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:A.122, D:K.147, D:K.147 Water bridges: D:C.121 GOL.41: 11 residues within 4Å: Chain D: D.35, W.37, N.38, D.72, K.147, R.205, D.209, V.210, D.262, N.263 Ligands: GOL.40 10 PLIP interactions: 10 interactions with chain D Hydrogen bonds: D:D.35, D:K.147, D:K.147, D:R.205, D:V.210, D:N.263 Water bridges: D:D.35, D:R.205, D:D.262, D:D.262 GOL.42: 9 residues within 4Å: Chain D: M.64, S.308, Q.309, A.310, N.399, V.401, I.419, L.420, Y.421 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:S.308, D:A.310, D:N.399, D:Y.421 Water bridges: D:S.311, D:V.401

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

NA.10: 3 residues within 4Å: Chain A: H.98, H.102 Ligands: BTB.11 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.102 NA.21: 3 residues within 4Å: Chain B: H.98, H.102 Ligands: BTB.22 No protein-ligand interaction detected (PLIP) NA.32: 3 residues within 4Å: Chain C: H.98, H.102 Ligands: BTB.33 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:H.102 NA.43: 3 residues within 4Å: Chain D: H.98, H.102 Ligands: BTB.44 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:H.98

4 x BTB: 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-covalent)

BTB.11: 6 residues within 4Å: Chain A: E.46, N.94, H.98, H.102 Ligands: NAG.3, NA.10 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.46, A:N.94 BTB.22: 6 residues within 4Å: Chain B: E.46, N.94, H.98, H.102 Ligands: NAG.14, NA.21 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.46, B:N.94 BTB.33: 6 residues within 4Å: Chain C: E.46, N.94, H.98, H.102 Ligands: NAG.25, NA.32 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:E.46, C:N.94 BTB.44: 6 residues within 4Å: Chain D: E.46, N.94, H.98, H.102 Ligands: NAG.36, NA.43 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:E.46, D:N.94

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

Related Entries With Identical Sequence