SMTL ID : 4j3u.1 (1 other biounit)

Crystal structure of barley limit dextrinase in complex with maltosyl-S-betacyclodextrin

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

monomer

Ligands

1 x SGD- GLC- GLC- GLC- GLC- GLC- GLC- GLC- GLC: Cyclic alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-[alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-1)]6-thio-alpha-D-glucopyranose

SGD-GLC-GLC-GLC-GLC-GLC-GLC-GLC-GLC.1: 14 residues within 4Å: Chain A: S.457, L.494, W.532, F.534, A.535, D.561, R.564, D.565, N.571, P.572, F.573, F.640, N.663, R.717 3 PLIP interactions: 3 interactions with chain A Water bridges: A:A.535, A:A.535 Hydrogen bonds: A:D.561, A:R.564, A:R.564

20 x IOD: IODIDE ION(Non-functional Binders)

IOD.2: 3 residues within 4Å: Chain A: M.24, G.443, R.448 Ligand excluded by PLIP IOD.3: 3 residues within 4Å: Chain A: T.514, T.515, D.521 Ligand excluded by PLIP IOD.4: 2 residues within 4Å: Chain A: E.851, G.894 Ligand excluded by PLIP IOD.5: 2 residues within 4Å: Chain A: D.681, E.682 Ligand excluded by PLIP IOD.6: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP IOD.7: 3 residues within 4Å: Chain A: R.825, P.829, E.830 Ligand excluded by PLIP IOD.8: 1 residues within 4Å: Chain A: S.73 Ligand excluded by PLIP IOD.9: 3 residues within 4Å: Chain A: H.688, I.781, Q.870 Ligand excluded by PLIP IOD.10: 4 residues within 4Å: Chain A: H.287, V.345, E.347, W.725 Ligand excluded by PLIP IOD.11: 2 residues within 4Å: Chain A: T.147, R.472 Ligand excluded by PLIP IOD.12: 2 residues within 4Å: Chain A: F.586, R.601 Ligand excluded by PLIP IOD.13: 1 residues within 4Å: Chain A: P.182 Ligand excluded by PLIP IOD.14: 3 residues within 4Å: Chain A: N.239, A.333, S.434 Ligand excluded by PLIP IOD.15: 3 residues within 4Å: Chain A: P.354, S.357, K.756 Ligand excluded by PLIP IOD.16: 2 residues within 4Å: Chain A: H.867, P.868 Ligand excluded by PLIP IOD.17: 2 residues within 4Å: Chain A: Y.304, A.306 Ligand excluded by PLIP IOD.18: 2 residues within 4Å: Chain A: P.868, N.872 Ligand excluded by PLIP IOD.19: 1 residues within 4Å: Chain A: S.853 Ligand excluded by PLIP IOD.20: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP IOD.21: 3 residues within 4Å: Chain A: L.479, N.480, N.484 Ligand excluded by PLIP

2 x CA: CALCIUM ION(Non-covalent)

CA.22: 3 residues within 4Å: Chain A: S.317, L.321, G.413 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:S.317, A:L.321, A:G.413, H2O.13, H2O.14 CA.23: 4 residues within 4Å: Chain A: Q.368, D.371, Y.373, N.721 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:Q.368, A:D.371, A:Y.373, H2O.1, H2O.9

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.24: 2 residues within 4Å: Chain A: R.282, R.296 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Moeller, M.S. et al., Oligosaccharide and substrate binding in the starch debranching enzyme barley limit dextrinase. J.Mol.Biol. (2015)

Release Date

2014-02-12

Peptides

Limit dextrinase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Limit dextrinase

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