SMTL ID : 8orp.1 (1 other biounit)

Crystal structure of Drosophila melanogaster alpha-amylase in complex with the inhibitor acarbose

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

monomer

Ligands

1 x BGC- GLC- RY7: 4,6-dideoxy-4-{[(1S,2S,3S,4R,5R)-2,3,4-trihydroxy-5-(hydroxymethyl)cyclohexyl]amino}-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-beta-D-glucopyranose

BGC-GLC-RY7.1: 19 residues within 4Å: Chain A: W.74, Y.78, H.117, Y.158, L.172, R.202, D.204, A.205, K.207, H.208, E.241, I.243, M.245, E.248, H.305, D.306, G.312, A.313 Ligands: GLC-RY7.2 11 PLIP interactions: 11 interactions with chain A Water bridges: A:I.243, A:M.245, A:I.243, A:M.245, A:D.306, A:D.306 Hydrogen bonds: A:Y.158, A:K.207, A:K.207, A:E.248, A:H.117, A:R.202, A:R.202, A:A.205, A:H.208, A:H.208, A:E.241, A:D.306, A:D.306

1 x GLC- RY7: 4,6-dideoxy-4-{[(1S,2S,3S,4R,5R)-2,3,4-trihydroxy-5-(hydroxymethyl)cyclohexyl]amino}-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose(Non-covalent)

GLC-RY7.2: 11 residues within 4Å: Chain A: W.74, W.75, Y.78, Q.79, A.120, D.121, V.170, G.171, D.306, H.311 Ligands: BGC-GLC-RY7.1 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.79, A:D.306, A:H.311, A:D.121, A:V.170 Water bridges: A:G.312, A:D.121, A:D.121 Hydrophobic interactions: A:A.120

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

CL.3: 5 residues within 4Å: Chain A: R.202, E.241, T.262, N.304, R.343 Ligand excluded by PLIP

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

EDO.4: 2 residues within 4Å: Chain A: K.325, Q.326 Ligand excluded by PLIP EDO.5: 3 residues within 4Å: Chain A: W.407, W.408, D.409 Ligand excluded by PLIP EDO.6: 5 residues within 4Å: Chain A: N.391, S.454, K.455, H.489, A.492 Ligand excluded by PLIP EDO.7: 4 residues within 4Å: Chain A: K.328, W.386, Q.388 Ligands: EDO.8 Ligand excluded by PLIP EDO.8: 5 residues within 4Å: Chain A: R.385, W.386, R.387, Q.388 Ligands: EDO.7 Ligand excluded by PLIP EDO.9: 6 residues within 4Å: Chain A: R.275, N.307, Q.308, G.315, V.318, T.320 Ligand excluded by PLIP EDO.10: 4 residues within 4Å: Chain A: T.360, A.366, S.367, I.369 Ligand excluded by PLIP EDO.11: 5 residues within 4Å: Chain A: N.410, G.411, S.412, Y.432 Ligands: EDO.16 Ligand excluded by PLIP EDO.12: 4 residues within 4Å: Chain A: S.437, R.472, A.473, S.474 Ligand excluded by PLIP EDO.13: 5 residues within 4Å: Chain A: T.464, S.474, I.475, N.476, L.486 Ligand excluded by PLIP EDO.14: 4 residues within 4Å: Chain A: S.295, D.296, P.338, G.340 Ligand excluded by PLIP EDO.15: 3 residues within 4Å: Chain A: A.294, D.296, R.297 Ligand excluded by PLIP EDO.16: 3 residues within 4Å: Chain A: Q.281, G.411 Ligands: EDO.11 Ligand excluded by PLIP EDO.17: 5 residues within 4Å: Chain A: G.27, R.28, R.396, N.397, G.400 Ligand excluded by PLIP EDO.18: 4 residues within 4Å: Chain A: S.135, S.136, K.137, S.146 Ligand excluded by PLIP EDO.19: 3 residues within 4Å: Chain A: S.145, D.148, Y.181 Ligand excluded by PLIP EDO.20: 4 residues within 4Å: Chain A: D.40, Q.94, S.97, R.101 Ligand excluded by PLIP EDO.21: 2 residues within 4Å: Chain A: K.100, H.228 Ligand excluded by PLIP

2 x SR: STRONTIUM ION(Non-functional Binders)

SR.22: 4 residues within 4Å: Chain A: N.116, R.165, D.174, H.208 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:R.165, A:D.174, A:H.208, H2O.2, H2O.3 SR.23: 1 residues within 4Å: Chain A: Q.281 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Rhimi, M. et al., Structural and Functional Characterization of Drosophila melanogaster alpha-Amylase. Molecules (2023)

Release Date

2023-08-16

Peptides

Alpha-amylase A: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Alpha-amylase A

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