SMTL ID : 1uh3.1

Thermoactinomyces vulgaris R-47 alpha-amylase/acarbose complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

monomer

Ligands

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

GLC-BGC.1: 7 residues within 4Å: Chain A: S.182, H.221, Y.223, F.313, D.516, R.520 Ligands: ACI.7 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.182, A:S.182, A:D.516, A:R.520, A:R.520

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

GLC-GLD.2: 10 residues within 4Å: Chain A: F.310, A.357, Q.359, Y.360, E.396, W.398, Y.433, Q.434, D.472 Ligands: ACI.7 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.359, A:Y.360, A:Y.433, A:Q.434, A:A.357, A:Y.360, A:Y.360 Water bridges: A:Q.359 Hydrophobic interactions: A:F.310 GLC-GLD.4: 5 residues within 4Å: Chain A: D.418, W.448, G.451, T.452 Ligands: HSD.8 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:T.452 Hydrogen bonds: A:D.418, A:W.448 GLC-GLD.6: 7 residues within 4Å: Chain A: K.40, G.41, I.43, W.65, N.68, D.75 Ligands: ACI.9 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.40, A:N.68, A:N.68, A:G.41, A:D.75, A:D.75 Water bridges: A:D.42, A:D.75

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.3: 11 residues within 4Å: Chain A: W.51, F.58, Y.89, R.91, A.115, D.116, D.117, Y.119, N.402, P.403 Ligands: HSD.8 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.116 Water bridges: A:N.400

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

GLC-GLC.5: 6 residues within 4Å: Chain A: W.485, S.587, V.588, S.589, D.628, G.629 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:V.588, A:G.629, A:G.629

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

ACI.7: 10 residues within 4Å: Chain A: Y.223, H.267, F.310, R.354, D.356, E.396, H.471, D.472 Ligands: GLC-BGC.1, GLC-GLD.2 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:F.310 Hydrogen bonds: A:H.267, A:R.354, A:R.354, A:E.396, A:E.396, A:H.471 Water bridges: A:D.472, A:D.472 ACI.9: 4 residues within 4Å: Chain A: N.3, I.43, T.44 Ligands: GLC-GLD.6 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.3, A:I.43

1 x HSD: (1S,2S,3R,6R)-6-amino-4-(hydroxymethyl)cyclohex-4-ene-1,2,3-triol(Non-covalent)

HSD.8: 6 residues within 4Å: Chain A: N.400, D.418, G.451, N.455 Ligands: GLC-GLC-GLC-GLC.3, GLC-GLD.4 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.400, A:D.418 Water bridges: A:N.400

3 x CA: CALCIUM ION(Non-covalent)

CA.10: 5 residues within 4Å: Chain A: A.2, D.4, N.6, D.42, D.96 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:A.2, A:D.4, A:N.6, A:D.42, A:D.96 CA.11: 6 residues within 4Å: Chain A: N.145, D.147, N.150, D.151, G.187, D.189 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.147, A:D.151, A:G.187, A:D.189 CA.12: 5 residues within 4Å: Chain A: D.276, N.279, F.281, S.283, E.288 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.276, A:F.281, A:S.283, A:E.288, H2O.8

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Abe, A. et al., Complex Structures of Thermoactinomyces vulgaris R-47 alpha-Amylase 1 with Malto-oligosaccharides Demonstrate the Role of Domain N Acting as a Starch-binding Domain. J.Mol.Biol. (2004)

Release Date

2004-01-13

Peptides

alpha-amylase I: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

alpha-amylase I

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