SMTL ID : 2y4s.1

BARLEY LIMIT DEXTRINASE IN COMPLEX WITH BETA-CYCLODEXTRIN

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

monomer

Ligands

1 x GLC- GLC- GLC- GLC- GLC- GLC- GLC: Cycloheptakis-(1-4)-(alpha-D-glucopyranose)(Non-functional Binders)

GLC-GLC-GLC-GLC-GLC-GLC-GLC.1: 12 residues within 4Å: Chain A: L.473, W.511, F.513, D.540, R.543, D.544, N.550, P.551, F.552, D.620, N.642, R.696 2 PLIP interactions: 2 interactions with chain A Water bridges: A:R.696, A:R.696

7 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 2 residues within 4Å: Chain A: D.297, K.762 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.762, A:K.762 Water bridges: A:D.297 GOL.3: 11 residues within 4Å: Chain A: E.257, H.304, R.470, E.509, W.511, F.538, Y.636, A.639, H.640, D.641, F.681 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:E.257, A:R.470, A:D.641 Water bridges: A:E.257, A:R.470, A:R.543, A:H.640 GOL.4: 7 residues within 4Å: Chain A: Y.356, V.400, H.403, A.437, A.438, D.472, L.473 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.403, A:E.509 Water bridges: A:R.470 GOL.5: 7 residues within 4Å: Chain A: C.94, Q.95, L.96, G.112, L.113, L.115, Y.195 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:L.96, A:L.96, A:L.113, A:Y.195 Water bridges: A:V.92, A:C.94 GOL.6: 9 residues within 4Å: Chain A: N.218, H.310, F.311, A.312, V.314, D.316, V.359, K.365, S.413 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.316, A:I.412 GOL.7: 9 residues within 4Å: Chain A: K.322, F.323, V.324, I.346, D.350, P.351, G.702, D.703, W.704 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:V.324, A:D.350, A:D.703, A:D.703, A:W.704 Water bridges: A:V.324 GOL.8: 4 residues within 4Å: Chain A: K.479, R.480, M.483, I.523 4 PLIP interactions: 4 interactions with chain A Water bridges: A:K.479, A:K.479, A:R.480, A:R.480

2 x CA: CALCIUM ION(Non-covalent)

CA.9: 4 residues within 4Å: Chain A: Q.347, D.350, Y.352, N.700 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:Q.347, A:D.350, A:Y.352, H2O.8, H2O.9 CA.10: 3 residues within 4Å: Chain A: S.296, L.300, G.392 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:S.296, A:S.296, A:L.300, A:G.392, H2O.1

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

IOD.11: 3 residues within 4Å: Chain A: T.493, T.494, D.500 Ligand excluded by PLIP IOD.12: 1 residues within 4Å: Chain A: H.141 Ligand excluded by PLIP IOD.13: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP IOD.14: 1 residues within 4Å: Chain A: K.486 Ligand excluded by PLIP IOD.15: 1 residues within 4Å: Chain A: H.846 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Vester-Christensen, M.B. et al., Crystal Structure of an Essential Enzyme in Seed Starch Degradation: Barley Limit Dextrinase in Complex with Cyclodextrins. J.Mol.Biol. (2010)

Release Date

2011-01-19

Peptides

LIMIT DEXTRINASE: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

LIMIT DEXTRINASE

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