SMTL ID : 3ede.1

Structural base for cyclodextrin hydrolysis

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.71 Å

Oligo State

homo-dimer

Ligands

4 x CA: CALCIUM ION(Non-covalent)

CA.1: 4 residues within 4Å: Chain A: S.222, T.270, D.280, Y.315 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:T.270, A:D.280, A:Y.315, H2O.3, H2O.3 CA.2: 6 residues within 4Å: Chain A: N.119, D.121, N.124, D.125, G.144, D.146 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.121, A:D.125, A:G.144, A:D.146, H2O.5 CA.6: 4 residues within 4Å: Chain B: S.222, T.270, D.280, Y.315 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:S.222, B:T.270, B:Y.315, H2O.25, H2O.27 CA.7: 6 residues within 4Å: Chain B: N.119, D.121, N.124, D.125, G.144, D.146 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.121, B:D.125, B:G.144, B:D.146, H2O.29

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 6 residues within 4Å: Chain A: H.181, Y.183, R.464, D.466, R.470 Ligands: GOL.4 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.464, A:D.466, A:R.470, A:R.470 Water bridges: A:H.181 GOL.4: 7 residues within 4Å: Chain A: Y.183, H.223, F.274, D.311, T.312 Ligands: GOL.3, GOL.5 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.223, A:E.340 Water bridges: A:R.309 GOL.5: 6 residues within 4Å: Chain A: F.274, T.312, E.340, D.418, R.464 Ligands: GOL.4 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:D.418, A:R.464, A:R.464 Water bridges: A:R.253, A:R.253, A:R.309 GOL.8: 5 residues within 4Å: Chain B: H.181, Y.183, D.466, R.470 Ligands: GOL.9 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:R.470, B:R.470 Water bridges: B:H.181, B:H.181, B:D.418 GOL.9: 8 residues within 4Å: Chain B: Y.183, H.223, F.274, D.311, T.312, E.340 Ligands: GOL.8, GOL.10 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:H.223, B:E.340 Water bridges: B:R.309 GOL.10: 5 residues within 4Å: Chain B: F.274, T.312, E.340, W.342 Ligands: GOL.9 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.340 Water bridges: B:R.253, B:R.253, B:E.340

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Buedenbender, S. et al., Structural base for enzymatic cyclodextrin hydrolysis. J.Mol.Biol. (2009)

Release Date

2009-03-03

Peptides

Cyclomaltodextrinase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Cyclomaltodextrinase