SMTL ID : 8cqf.1

Crystal Structure of a Chimeric Alpha-Amylase from Pseudoalteromonas Haloplanktis Complexed with Rearranged Acarbose

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.05 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: 15 residues within 4Å: Chain A: P.2, T.3, A.30, Y.82, V.196, L.219, S.253, S.254, A.256, Y.297, G.298, Y.299, R.350, A.354, W.357 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:Y.299 Hydrogen bonds: A:G.298, A:S.253, A:W.357 Water bridges: A:D.80, A:Y.299, A:Y.299, A:R.350, A:S.254 GLC-GLC-AC1.3: 7 residues within 4Å: Chain A: G.282, R.283, D.286, F.330, R.339, W.340, S.341 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:F.330, A:F.330 Hydrogen bonds: A:S.341, A:S.341, A:R.283 Water bridges: A:R.283, A:R.283, A:Y.342

1 x ASO- 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)-1,5-anhydro-D-glucitol(Non-covalent)

ASO-AC1.2: 8 residues within 4Å: Chain A: F.108, P.109, I.110, Y.111, S.112, Q.114, D.115, Y.151 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.111, A:S.112, A:S.112, A:D.115, A:D.115 Water bridges: A:S.149

1 x GLC- AC1- GLC- GLC: alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-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

GLC-AC1-GLC-GLC.4: 26 residues within 4Å: Chain A: W.46, W.47, T.48, Y.50, Q.51, L.86, H.89, A.92, Y.127, L.139, V.140, G.141, L.142, R.172, D.174, A.175, K.177, H.178, E.200, I.202, E.207, H.263, D.264, H.269, G.270, W.313 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.89, A:R.172, A:R.172, A:D.174, A:A.175, A:E.200, A:E.200, A:H.263, A:D.264, A:Q.51 Water bridges: A:D.264, A:D.264

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.5: 6 residues within 4Å: Chain A: R.172, E.200, T.221, F.223, N.262, R.301 Ligand excluded by PLIP CL.6: 3 residues within 4Å: Chain A: E.56, L.57, R.64 Ligand excluded by PLIP

1 x CA: CALCIUM ION(Non-covalent)

CA.7: 7 residues within 4Å: Chain A: N.88, H.117, Q.135, N.136, D.144, H.178, V.179 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:Q.135, A:D.144, A:H.178, H2O.2, H2O.6

1 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.8: 8 residues within 4Å: Chain A: Q.18, Q.22, V.321, H.322, N.323, G.325, N.326, L.327 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.22 Water bridges: A:Q.18, A:H.322

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

van der Ent, F. et al., Computational design of the temperature optimum of an enzyme reaction. Sci Adv (2023)

Release Date

2023-06-21

Peptides

Alpha-amylase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Alpha-amylase