SMTL ID : 3bc9.1

Alpha-amylase B in complex with acarbose

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.35 Å

Oligo State

monomer

Ligands

1 x GLC- G6D: alpha-D-quinovopyranose-(1-4)-alpha-D-glucopyranose(Non-covalent)

GLC-G6D.1: 7 residues within 4Å: Chain A: K.198, M.235, G.236, A.237, W.260, W.287 Ligands: ACI.10 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:A.237, A:G.236, A:A.237 Water bridges: A:W.260, A:A.318

1 x GLC- GLD: 4,6-dideoxy-alpha-D-xylo-hexopyranose-(1-4)-alpha-D-glucopyranose(Non-covalent)

GLC-GLD.2: 9 residues within 4Å: Chain A: W.131, Y.184, G.185, M.235, M.316, R.450, Y.455 Ligands: ACI.10, ACI.11 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.450, A:R.450, A:Y.455 Water bridges: A:D.181, A:G.185, A:G.185

1 x BGC- GLC- GLD: 4,6-dideoxy-alpha-D-xylo-hexopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-beta-D-glucopyranose

BGC-GLC-GLD.3: 9 residues within 4Å: Chain A: A.351, K.353, H.354, E.380, W.382, E.384, D.447, Y.455 Ligands: ACI.11 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:K.353, A:K.353, A:A.351, A:H.354, A:K.353, A:E.384, A:Y.455 Hydrophobic interactions: A:Y.455 Water bridges: A:E.380, A:W.382, A:K.353, A:W.382, A:D.385

1 x GLC- GLC- AC1: 4,6-dideoxy-4-{[(1S,4R,5S,6S)-4,5,6-trihydroxy-3-(hydroxymethyl)cyclohex-2-en-1-yl]amino}-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose

GLC-GLC-AC1.4: 11 residues within 4Å: Chain A: D.449, S.458, I.459, Y.460, S.461, R.462, K.463, Y.464, W.488, E.588, D.589 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:S.458, A:S.458, A:D.449, A:I.459, A:Y.460, A:R.462, A:K.463, A:E.588, A:E.588, A:E.588 Hydrophobic interactions: A:Y.464 Water bridges: A:Y.464

4 x CA: CALCIUM ION(Non-covalent)

CA.5: 5 residues within 4Å: Chain A: D.283, S.303, D.305, D.321, E.323 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.283, A:S.303, A:D.305, A:D.321, A:E.323 CA.6: 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.2 CA.7: 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.4 CA.9: 3 residues within 4Å: Chain A: F.527, V.530, D.533 6 PLIP interactions: 3 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:F.527, A:V.530, A:D.533, H2O.16, H2O.16, H2O.16

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

NA.8: 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

2 x ACI: 6-AMINO-4-HYDROXYMETHYL-CYCLOHEX-4-ENE-1,2,3-TRIOL(Non-covalent)

ACI.10: 6 residues within 4Å: Chain A: M.235, D.286, M.316, G.317 Ligands: GLC-G6D.1, GLC-GLD.2 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.286, A:G.317 Water bridges: A:D.286 ACI.11: 13 residues within 4Å: Chain A: W.131, Y.184, V.230, H.233, M.316, R.348, D.350, E.380, H.446, D.447, R.450 Ligands: GLC-GLD.2, BGC-GLC-GLD.3 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:H.233, A:R.348, A:R.348, A:D.350, A:E.380, A:D.447, A:R.450

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

GLC.12: 7 residues within 4Å: Chain A: W.304, D.305, W.306, T.307, N.309, W.310, D.311 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.307, A:T.307, A:D.311 Water bridges: A:W.304, A:E.312 GLC.13: 2 residues within 4Å: Chain A: Y.239, N.264 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.264

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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