SMTL ID : 6toz.1

Crystal structure of Bacillus paralicheniformis alpha-amylase in complex with acarbose

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.94 Å

Oligo State

monomer

Ligands

2 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-AC1.1: 20 residues within 4Å: Chain A: W.13, Y.56, H.105, E.189, Y.193, L.196, R.229, D.231, A.232, K.234, H.235, E.261, W.263, Q.264, N.265, Y.290, H.327, D.328, S.334, L.335 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:H.105, A:R.229, A:D.231, A:A.232, A:H.235, A:H.235, A:E.261, A:E.189, A:K.234, A:K.234, A:Q.264 Water bridges: A:E.261, A:W.263, A:D.328, A:Y.193 GLC-GLC-AC1.2: 12 residues within 4Å: Chain A: G.5, T.38, N.96, Y.98, E.255, F.257, P.317, V.318, E.355, A.356, G.357, Y.358 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:Y.358, A:Y.358 Hydrogen bonds: A:T.38, A:T.38, A:E.255, A:V.318, A:P.317, A:E.355, A:G.357 Water bridges: A:N.96, A:N.96, A:E.255, A:E.255, A:S.282

2 x CA: CALCIUM ION(Non-covalent)

CA.3: 5 residues within 4Å: Chain A: N.104, D.194, D.200, H.235 Ligands: NA.5 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.194, A:D.194, A:D.200, A:H.235, H2O.7 CA.4: 5 residues within 4Å: Chain A: D.161, A.181, D.183, D.202, D.204 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.161, A:A.181, A:D.202, A:D.204, H2O.14

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

NA.5: 7 residues within 4Å: Chain A: D.161, D.183, D.194, D.200, I.201, D.202 Ligands: CA.3 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.161, A:D.200 Water bridges: A:I.201 NA.6: 5 residues within 4Å: Chain A: G.300, Y.302, H.406, N.407, D.430 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.406, A:N.407

3 x ACY: ACETIC ACID(Non-functional Binders)

ACY.7: 2 residues within 4Å: Chain A: N.188, G.191 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.126, A:N.188 ACY.8: 3 residues within 4Å: Chain A: R.437, N.463, W.467 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.463 Salt bridges: A:R.437 ACY.9: 2 residues within 4Å: Chain A: Y.439, R.442 2 PLIP interactions: 2 interactions with chain A Water bridges: A:R.442 Salt bridges: A:R.442

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bozic, N. et al., Characterization of the starch surface binding site on Bacillus paralicheniformis alpha-amylase. Int.J.Biol.Macromol. (2020)

Release Date

2020-10-14

Peptides

Amylase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Amylase

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