SMTL ID : 3edf.1

Structural base for cyclodextrin hydrolysis

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.65 Å

Oligo State

homo-dimer

Ligands

2 x BGC- BGC- BGC- BGC- BGC- BGC: beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose(Non-covalent)(Post Translational Modification)

BGC-BGC-BGC-BGC-BGC-BGC.1: 24 residues within 4Å: Chain A: H.181, Y.183, H.223, R.253, F.274, V.275, M.278, R.309, D.311, T.312, Y.315, Q.340, W.342, H.417, D.418, R.464, D.466, R.470 Ligands: GLC-GLC-GLC-GLC-GLC-GLC.2, GLC-GLC-GLC-GLC-GLC-GLC.2, GLC-GLC-GLC-GLC-GLC-GLC.2, GLC-GLC-GLC-GLC-GLC-GLC.2, GLC-GLC-GLC-GLC-GLC-GLC.2, GLC-GLC-GLC-GLC-GLC-GLC.2 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.464 Water bridges: A:R.464 BGC-BGC-BGC-BGC-BGC-BGC.3: 24 residues within 4Å: Chain B: H.181, Y.183, H.223, R.253, F.274, V.275, M.278, R.309, D.311, T.312, Y.315, Q.340, W.342, H.417, D.418, R.464, D.466, R.470 Ligands: GLC-GLC-GLC-GLC-GLC-GLC.4, GLC-GLC-GLC-GLC-GLC-GLC.4, GLC-GLC-GLC-GLC-GLC-GLC.4, GLC-GLC-GLC-GLC-GLC-GLC.4, GLC-GLC-GLC-GLC-GLC-GLC.4, GLC-GLC-GLC-GLC-GLC-GLC.4 No protein-ligand interaction detected (PLIP)

2 x GLC- GLC- GLC- GLC- GLC- GLC: Cyclohexakis-(1-4)-(alpha-D-glucopyranose)(Non-covalent)

GLC-GLC-GLC-GLC-GLC-GLC.2: 25 residues within 4Å: Chain A: H.181, Y.183, H.223, H.251, R.253, F.274, V.275, M.278, R.309, D.311, T.312, Y.315, Q.340, W.342, H.417, D.418, R.464, D.466, R.470 Ligands: BGC-BGC-BGC-BGC-BGC-BGC.1, BGC-BGC-BGC-BGC-BGC-BGC.1, BGC-BGC-BGC-BGC-BGC-BGC.1, BGC-BGC-BGC-BGC-BGC-BGC.1, BGC-BGC-BGC-BGC-BGC-BGC.1, BGC-BGC-BGC-BGC-BGC-BGC.1 2 PLIP interactions: 2 interactions with chain A Water bridges: A:R.464, A:D.466 GLC-GLC-GLC-GLC-GLC-GLC.4: 25 residues within 4Å: Chain B: H.181, Y.183, H.223, H.251, R.253, F.274, V.275, M.278, R.309, D.311, T.312, Y.315, Q.340, W.342, H.417, D.418, R.464, D.466, R.470 Ligands: BGC-BGC-BGC-BGC-BGC-BGC.3, BGC-BGC-BGC-BGC-BGC-BGC.3, BGC-BGC-BGC-BGC-BGC-BGC.3, BGC-BGC-BGC-BGC-BGC-BGC.3, BGC-BGC-BGC-BGC-BGC-BGC.3, BGC-BGC-BGC-BGC-BGC-BGC.3 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.253, B:R.464, B:R.464 Water bridges: B:R.253

4 x CA: CALCIUM ION(Non-covalent)

CA.5: 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:S.222, A:T.270, A:Y.315, H2O.1, H2O.3 CA.6: 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.4 CA.9: 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:D.280, B:D.280, H2O.30, H2O.30 CA.10: 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.31

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 10 residues within 4Å: Chain A: I.112, M.113, R.116, F.117, R.421, Y.450, S.451, R.470, R.471, F.473 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:M.113, A:R.421, A:S.451, A:S.451, A:R.471 GOL.8: 10 residues within 4Å: Chain A: A.118, N.119, G.120, G.149, D.152, H.153, G.475, G.476, W.477, A.478 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.152, A:D.152, A:G.475 Water bridges: A:N.119, A:A.478 GOL.11: 10 residues within 4Å: Chain B: I.112, M.113, R.116, F.117, R.421, Y.450, S.451, R.470, R.471, F.473 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:M.113, B:R.421, B:S.451, B:S.451, B:R.471 GOL.12: 9 residues within 4Å: Chain B: N.119, G.120, G.149, D.152, H.153, G.475, G.476, W.477, A.478 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.152, B:G.475

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

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