SMTL ID : 3a5v.1

Crystal structure of alpha-galactosidase I from Mortierella vinacea

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-tetramer

Ligands

4 x NAG- NAG- BMA- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-MAN-MAN-MAN.1: 14 residues within 4Å: Chain A: N.2, N.3, G.4, I.7, N.155, G.158, R.159, P.160 Chain D: N.57, E.58, L.99, G.103, H.104, I.105 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.2, A:N.2, A:N.2 Water bridges: A:G.4 NAG-NAG-BMA-MAN-MAN-MAN-MAN.9: 14 residues within 4Å: Chain B: N.2, N.3, G.4, I.7, N.155, G.158, R.159, P.160 Chain C: N.57, E.58, L.99, G.103, H.104, I.105 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.2, B:N.2, B:N.2 Water bridges: B:G.4 NAG-NAG-BMA-MAN-MAN-MAN-MAN.17: 14 residues within 4Å: Chain A: N.57, E.58, L.99, G.103, H.104, I.105 Chain C: N.2, N.3, G.4, I.7, N.155, G.158, R.159, P.160 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.2, C:N.2, C:N.2 Water bridges: C:G.4 NAG-NAG-BMA-MAN-MAN-MAN-MAN.25: 14 residues within 4Å: Chain B: N.57, E.58, L.99, G.103, H.104, I.105 Chain D: N.2, N.3, G.4, I.7, N.155, G.158, R.159, P.160 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.2, D:N.2, D:N.2 Water bridges: D:G.4

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: 1 residues within 4Å: Chain A: N.276 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 1 residues within 4Å: Chain B: N.276 No protein-ligand interaction detected (PLIP) NAG-NAG.18: 1 residues within 4Å: Chain C: N.276 No protein-ligand interaction detected (PLIP) NAG-NAG.26: 1 residues within 4Å: Chain D: N.276 No protein-ligand interaction detected (PLIP)

4 x NAG- NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA.3: 6 residues within 4Å: Chain A: S.357, I.358, E.359, N.371, M.391, D.392 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.392, A:D.392 NAG-NAG-BMA.11: 6 residues within 4Å: Chain B: S.357, I.358, E.359, N.371, M.391, D.392 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.392, B:D.392 NAG-NAG-BMA.19: 6 residues within 4Å: Chain C: S.357, I.358, E.359, N.371, M.391, D.392 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:D.392, C:D.392 NAG-NAG-BMA.27: 6 residues within 4Å: Chain D: S.357, I.358, E.359, N.371, M.391, D.392 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:D.392, D:D.392

16 x 1PG: 2-(2-{2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL(Non-covalent)

1PG.4: 11 residues within 4Å: Chain A: E.289, A.292, D.296, L.318, A.319, N.320, T.322, R.361, L.363, K.389, M.391 Ligand excluded by PLIP 1PG.5: 7 residues within 4Å: Chain A: N.279, K.282, E.283, M.286, N.287, W.364, Q.366 Ligand excluded by PLIP 1PG.6: 4 residues within 4Å: Chain A: K.63, G.109, Y.110, I.113 Ligand excluded by PLIP 1PG.7: 4 residues within 4Å: Chain A: N.317, Y.347, N.348 Chain D: R.214 Ligand excluded by PLIP 1PG.12: 11 residues within 4Å: Chain B: E.289, A.292, D.296, L.318, A.319, N.320, T.322, R.361, L.363, K.389, M.391 Ligand excluded by PLIP 1PG.13: 7 residues within 4Å: Chain B: N.279, K.282, E.283, M.286, N.287, W.364, Q.366 Ligand excluded by PLIP 1PG.14: 4 residues within 4Å: Chain B: K.63, G.109, Y.110, I.113 Ligand excluded by PLIP 1PG.15: 4 residues within 4Å: Chain B: N.317, Y.347, N.348 Chain C: R.214 Ligand excluded by PLIP 1PG.20: 11 residues within 4Å: Chain C: E.289, A.292, D.296, L.318, A.319, N.320, T.322, R.361, L.363, K.389, M.391 Ligand excluded by PLIP 1PG.21: 7 residues within 4Å: Chain C: N.279, K.282, E.283, M.286, N.287, W.364, Q.366 Ligand excluded by PLIP 1PG.22: 4 residues within 4Å: Chain C: K.63, G.109, Y.110, I.113 Ligand excluded by PLIP 1PG.23: 4 residues within 4Å: Chain A: R.214 Chain C: N.317, Y.347, N.348 Ligand excluded by PLIP 1PG.28: 11 residues within 4Å: Chain D: E.289, A.292, D.296, L.318, A.319, N.320, T.322, R.361, L.363, K.389, M.391 Ligand excluded by PLIP 1PG.29: 7 residues within 4Å: Chain D: N.279, K.282, E.283, M.286, N.287, W.364, Q.366 Ligand excluded by PLIP 1PG.30: 4 residues within 4Å: Chain D: K.63, G.109, Y.110, I.113 Ligand excluded by PLIP 1PG.31: 4 residues within 4Å: Chain B: R.214 Chain D: N.317, Y.347, N.348 Ligand excluded by PLIP

4 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.8: 8 residues within 4Å: Chain A: W.16, D.51, D.52, Y.93, C.101, G.102, K.127, D.129 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:W.16, A:D.52, A:D.52, A:K.127, A:D.129 Water bridges: A:D.189 TRS.16: 8 residues within 4Å: Chain B: W.16, D.51, D.52, Y.93, C.101, G.102, K.127, D.129 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:W.16, B:D.52, B:D.52, B:K.127, B:D.129 Water bridges: B:D.189 TRS.24: 8 residues within 4Å: Chain C: W.16, D.51, D.52, Y.93, C.101, G.102, K.127, D.129 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:W.16, C:D.52, C:D.52, C:K.127, C:D.129 Water bridges: C:D.189 TRS.32: 8 residues within 4Å: Chain D: W.16, D.51, D.52, Y.93, C.101, G.102, K.127, D.129 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:W.16, D:D.52, D:D.52, D:K.127, D:D.129 Water bridges: D:D.189

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fujimoto, Z. et al., The Tetramer Structure of the Glycoside Hydrolase Family 27 alpha-Galactosidase I from Umbelopsis vinacea. Biosci.Biotechnol.Biochem. (2009)

Release Date

2009-08-25

Peptides

Alpha-galactosidase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

Alpha-galactosidase