SMTL ID : 2f6d.1

Structure of the complex of a glucoamylase from Saccharomycopsis fibuligera with acarbose

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

monomer

Ligands

2 x GLC- GLC- AC1: 4,6-dideoxy-4-{[(1S,4R,5S,6S)-4,5,6-trihydroxy-3-(hydroxymethyl)cyclohex-2-en-1-yl]amino}-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose(Non-covalent)

GLC-GLC-AC1.1: 18 residues within 4Å: Chain A: A.54, Y.63, W.67, R.69, D.70, A.138, W.139, G.140, L.208, W.209, E.210, E.211, R.345, Y.351, W.362, E.456, L.471, W.473 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Y.63, A:Y.63, A:W.67, A:W.139 Hydrogen bonds: A:R.69, A:R.69, A:R.69, A:W.209, A:E.210, A:E.211, A:E.211, A:R.345, A:R.345, A:W.139, A:G.140 Water bridges: A:A.54, A:D.70, A:E.211 GLC-GLC-AC1.2: 9 residues within 4Å: Chain A: R.15, D.446, H.447, I.448, N.449, D.450, T.462, G.463, Y.464 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.449, A:D.450, A:G.463, A:H.447, A:T.462 Water bridges: A:D.450, A:S.465, A:S.465, A:S.465, A:S.465, A:S.465, A:S.465, A:Y.464

1 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.3: 7 residues within 4Å: Chain A: D.300, I.301, E.303, S.304, K.375, Y.378, D.379 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:I.301, A:I.301, A:E.303, A:S.304, A:D.310 Water bridges: A:S.305, A:K.375, A:K.375 Salt bridges: A:K.375

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

NA.4: 2 residues within 4Å: Chain A: S.305, D.310 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.305 NA.5: 1 residues within 4Å: Chain A: I.177 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:I.177 Water bridges: A:I.177

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sevcik, J. et al., Structure of the complex of a yeast glucoamylase with acarbose reveals the presence of a raw starch binding site on the catalytic domain. Febs J. (2006)

Release Date

2006-05-23

Peptides

Glucoamylase GLU1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Glucoamylase GLU1

Related Entries With Identical Sequence