SMTL ID : 3eqa.1

Catalytic domain of glucoamylase from aspergillus niger complexed with tris and glycerol

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

monomer

Ligands

1 x NAG- NAG- BMA- MAN: 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.1: 13 residues within 4Å: Chain A: W.170, N.171, Q.172, T.173, S.184, Y.223, S.226, W.228, T.229, F.237, C.449, A.450, A.451 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:W.228, A:S.226 Water bridges: A:W.228, A:Y.223, A:S.226, A:D.238

1 x NAG- NAG- BMA- MAN- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)]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-MAN.2: 17 residues within 4Å: Chain A: V.13, W.28, V.29, S.30, P.41, S.42, T.43, N.45, P.46, F.49, N.395, S.397, Q.409, S.411, A.412, R.413, D.414 3 PLIP interactions: 3 interactions with chain A Water bridges: A:R.413, A:S.399, A:Q.409, A:Q.409, A:Q.409, A:S.411, A:W.28, A:S.397, A:R.413 Hydrogen bonds: A:S.42, A:S.42, A:R.413, A:R.413

7 x MAN: alpha-D-mannopyranose(Post Translational Modification)

MAN.3: 7 residues within 4Å: Chain A: D.263, E.439, T.440, S.441, A.442, S.443, S.444 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:D.263, A:S.441, A:A.442, A:S.443, A:S.444 Water bridges: A:D.263 MAN.4: 3 residues within 4Å: Chain A: P.218, S.444, P.446 No protein-ligand interaction detected (PLIP) MAN.5: 4 residues within 4Å: Chain A: A.450, T.452, S.453 Ligands: MAN.6 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.453 Water bridges: A:Q.216, A:S.453 MAN.6: 5 residues within 4Å: Chain A: A.451, T.452, S.453, I.455 Ligands: MAN.5 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:A.451 MAN.7: 6 residues within 4Å: Chain A: P.157, R.160, S.459, S.460, V.461 Ligands: MAN.9 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.160 MAN.8: 7 residues within 4Å: Chain A: A.86, I.87, G.90, L.98, S.460, V.461 Ligands: MAN.9 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:A.86, A:G.90 Water bridges: A:A.86, A:V.461 MAN.9: 5 residues within 4Å: Chain A: S.460, V.461, T.462 Ligands: MAN.7, MAN.8 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.460, A:S.460

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

TRS.10: 10 residues within 4Å: Chain A: A.39, Y.48, W.52, R.54, D.55, L.177, W.178, E.179, W.417 Ligands: GOL.11 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.54, A:R.54, A:E.179

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.11: 6 residues within 4Å: Chain A: Y.48, W.178, E.179, E.180, R.305 Ligands: TRS.10 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Y.48, A:E.180, A:R.305, A:R.305 Water bridges: A:E.180

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lee, J. et al., Structure of the catalytic domain of glucoamylase from Aspergillus niger. Acta Crystallogr.,Sect.F (2011)

Release Date

2009-10-13

Peptides

Glucoamylase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Glucoamylase