SMTL ID : 3bcd.1

Alpha-amylase B in complex with maltotetraose and alpha-cyclodextrin

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

monomer

Ligands

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

BGC-GLC-GLC-GLC.1: 13 residues within 4Å: Chain A: Y.184, H.233, R.348, D.350, A.351, K.353, H.354, E.380, W.382, E.384, H.446, D.447, Y.455 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.384, A:H.233, A:R.348, A:D.350, A:D.447 Water bridges: A:D.385, A:D.385

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.2: 12 residues within 4Å: Chain A: D.449, S.458, I.459, Y.460, S.461, R.462, K.463, Y.464, W.488, M.490, E.588, D.589 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:R.462, A:K.463, A:E.588, A:E.588 Water bridges: A:Y.464, A:Y.464, A:Y.464

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

GLC-GLC-GLC-GLC-GLC-GLC.3: 8 residues within 4Å: Chain A: M.176, A.177, K.198, G.236, A.237, W.260, W.287, D.289 No protein-ligand interaction detected (PLIP)

7 x CA: CALCIUM ION(Non-covalent)

CA.4: 5 residues within 4Å: Chain A: D.283, S.303, D.305, D.321, E.323 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:S.303, A:D.305, A:D.321, A:E.323, H2O.10 CA.5: 4 residues within 4Å: Chain A: N.232, D.313, D.319, H.354 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.313, A:D.313, A:D.319, A:H.354, H2O.1 CA.6: 4 residues within 4Å: Chain A: A.419, A.517, D.518, D.541 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:A.419, A:A.517, A:D.541, A:D.541, H2O.2 CA.8: 4 residues within 4Å: Chain A: G.526, F.527, V.530, D.533 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:F.527, A:V.530, A:D.533 CA.9: 4 residues within 4Å: Chain A: K.31, N.32, L.33, L.80 6 PLIP interactions: 1 interactions with chain A, 5 Ligand-Water interactions Metal complexes: A:K.31, H2O.3, H2O.5, H2O.6, H2O.7, H2O.10 CA.10: 3 residues within 4Å: Chain A: D.414, N.417, G.418 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.414, A:D.414, A:G.418, H2O.3, H2O.7 CA.11: 3 residues within 4Å: Chain A: Q.368, S.371, R.373 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:Q.368, A:S.371, A:R.373, H2O.7, H2O.7

1 x NA: SODIUM ION(Non-functional Binders)

NA.7: 6 residues within 4Å: Chain A: D.283, D.305, D.313, D.319, V.320, D.321 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.283, A:V.320 Water bridges: A:V.320

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tan, T.-C. et al., Crystal Structure of the Polyextremophilic alpha-Amylase AmyB from Halothermothrix orenii: Details of a Productive Enzyme-Substrate Complex and an N Domain with a Role in Binding Raw Starch. J.Mol.Biol. (2008)

Release Date

2008-04-22

Peptides

Alpha amylase, catalytic region: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Alpha amylase, catalytic region

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