SMTL ID : 7xoi.1 (7 other biounits)

Aspergillus sojae alpha-glucosidase AsojAgdL in complex with trehalose

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

hetero-1-1-mer

Ligands

2 x GLC- GLC: alpha-D-glucopyranose-(1-1)-alpha-D-glucopyranose(Non-covalent)

GLC-GLC.1: 16 residues within 4Å: Chain A: D.253, Y.255, Y.349, D.377, I.378, M.416, W.453, D.493, M.494, F.500, R.503 Chain B: R.111, D.127, F.161, H.186, E.188 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.503, A:R.503 GLC-GLC.3: 8 residues within 4Å: Chain B: Q.204, N.208, S.211, I.212, Q.215, W.286, D.308, I.309 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:I.309, B:I.309

1 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: 7 residues within 4Å: Chain A: A.359, V.360, N.363, D.533, A.534 Chain B: Y.197, R.198 No protein-ligand interaction detected (PLIP)

1 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.4: 10 residues within 4Å: Chain A: T.333, P.334, L.335, M.336 Chain B: H.94, R.98, K.119, N.228, Q.229, V.361 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.98, B:R.98

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

NAG.5: 2 residues within 4Å: Chain A: L.129, N.152 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.152 NAG.6: 4 residues within 4Å: Chain A: N.241, Y.245, G.260 Ligands: NAG.7 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:Y.245 Hydrogen bonds: A:N.241 Water bridges: A:D.236 NAG.7: 2 residues within 4Å: Chain A: N.244 Ligands: NAG.6 No protein-ligand interaction detected (PLIP) NAG.8: 3 residues within 4Å: Chain A: E.442, N.444, S.446 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.444, A:S.446, A:S.446 NAG.9: 4 residues within 4Å: Chain A: N.508, F.515, V.518, D.519 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.515, A:V.518, A:D.519 Hydrogen bonds: A:N.508 NAG.12: 5 residues within 4Å: Chain B: G.163, N.164, E.188, Y.190, N.192 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Y.190, B:N.192 NAG.13: 4 residues within 4Å: Chain A: S.365, R.409, Q.411 Chain B: N.327 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Water bridges: A:L.371 Hydrogen bonds: B:N.327

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

NA.10: 7 residues within 4Å: Chain B: S.130, G.160, F.161, G.162, G.163, A.191, Q.194 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.130, B:C.159, B:Q.194 Water bridges: B:V.165

1 x GLC: alpha-D-glucopyranose(Non-covalent)

GLC.11: 5 residues within 4Å: Chain A: F.479, D.480, D.486 Chain B: R.100, R.101 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:D.480, B:R.101, B:R.101

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ding, Y. et al., Structural basis for proteolytic processing of Aspergillus sojae alpha-glucosidase L with strong transglucosylation activity. J.Struct.Biol. (2022)

Release Date

2022-06-15

Peptides

alpha-glucosidase N-terminal polypeptide: A
alpha-glucosidase C-terminal polypeptide: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

alpha-glucosidase N-terminal polypeptide

alpha-glucosidase C-terminal polypeptide

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