SMTL ID : 4j3v.1

Crystal structure of barley limit dextrinase in complex with a branched thio-linked hexasaccharide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.45 Å

Oligo State

monomer

Ligands

1 x GLC- GLC- GLC- GLC: alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose

GLC-GLC-GLC-GLC.1: 15 residues within 4Å: Chain A: L.494, E.530, W.532, F.534, D.561, R.564, F.573, D.662, N.663, R.717, D.718, K.747 Ligands: GLC-GLC-SGD-GLC-GLC-GLC.2, GLC-GLC-SGD-GLC-GLC-GLC.2, GLC-GLC-SGD-GLC-GLC-GLC.2 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.717, A:D.718, A:K.747 Water bridges: A:D.662, A:D.662

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

GLC-GLC-SGD-GLC-GLC-GLC.2: 20 residues within 4Å: Chain A: E.369, W.375, Y.377, N.378, H.424, D.426, N.456, A.459, M.460, R.491, D.493, L.494, E.530, H.661, D.662, D.718, Y.720, K.747 Ligands: GLC-GLC-GLC-GLC.1, GLC-GLC-GLC-GLC.1 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.456, A:Y.720, A:K.747, A:K.747 Water bridges: A:S.457, A:A.459, A:A.459, A:Y.720

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

IOD.3: 2 residues within 4Å: Chain A: G.443, R.448 Ligand excluded by PLIP IOD.4: 2 residues within 4Å: Chain A: T.147, R.472 Ligand excluded by PLIP IOD.5: 2 residues within 4Å: Chain A: H.688, Q.870 Ligand excluded by PLIP IOD.6: 2 residues within 4Å: Chain A: N.239, S.434 Ligand excluded by PLIP IOD.7: 1 residues within 4Å: Chain A: S.73 Ligand excluded by PLIP IOD.8: 2 residues within 4Å: Chain A: F.586, R.601 Ligand excluded by PLIP IOD.9: 1 residues within 4Å: Chain A: H.867 Ligand excluded by PLIP IOD.10: 2 residues within 4Å: Chain A: R.501, M.504 Ligand excluded by PLIP IOD.11: 2 residues within 4Å: Chain A: P.849, H.850 Ligand excluded by PLIP

1 x CA: CALCIUM ION(Non-covalent)

CA.12: 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.3, H2O.7

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

CL.13: 3 residues within 4Å: Chain A: P.354, S.357, K.756 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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