SMTL ID : 6z8l.1

Alpha-Amylase in complex with probe fragments

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.40 Å

Oligo State

monomer

Ligands

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

GLC-GLC.1: 14 residues within 4Å: Chain A: W.58, W.59, E.60, Y.62, Q.63, G.104, V.107, T.163, G.164, L.165, D.300, H.305, G.306 Ligands: GLC-GLC.2 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.63 GLC-GLC.2: 13 residues within 4Å: Chain A: Y.151, L.162, T.163, A.198, K.200, H.201, E.233, I.235, E.240, D.300, G.306, A.307 Ligands: GLC-GLC.1 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.200, A:E.240 Water bridges: A:I.235 GLC-GLC.3: 6 residues within 4Å: Chain A: K.261, E.272, Y.276, N.279, G.283, W.284 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.272, A:N.279, A:G.283 Water bridges: A:K.261 GLC-GLC.4: 2 residues within 4Å: Chain A: N.53, P.54 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.53

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

GLC.5: 6 residues within 4Å: Chain A: K.140, E.171, R.176, W.203, G.205, D.206 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.140, A:E.171, A:R.176, A:G.205 Water bridges: A:E.171

1 x CA: CALCIUM ION(Non-covalent)

CA.6: 6 residues within 4Å: Chain A: N.100, N.137, R.158, D.167, H.201, M.202 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:R.158, A:D.167, A:H.201, H2O.4, H2O.7

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

CL.7: 6 residues within 4Å: Chain A: R.195, E.233, T.254, F.256, N.298, R.337 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Axer, A. et al., Enhancing glycan stability via site-selective fluorination: modulating substrate orientation by molecular design. Chem Sci (2020)

Release Date

2020-12-02

Peptides

Pancreatic alpha-amylase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Pancreatic alpha-amylase

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