SMTL ID : 6yqa.1 (1 other biounit)

Taka-amylase in complex with alpha-glucosyl epi-cyclophellitol aziridine inhibitor

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.67 Å

Oligo State

monomer

Ligands

1 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.1: 7 residues within 4Å: Chain A: I.108, Y.109, W.211, S.214, L.215, N.218, Y.219 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.215 Hydrogen bonds: A:S.214, A:N.218

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

EDO.2: 8 residues within 4Å: Chain A: T.94, A.95, D.147, G.148, A.149, N.190, T.191, V.192 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.95, A:T.191 EDO.3: 5 residues within 4Å: Chain A: H.355, Y.356, A.357, G.358, E.366 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:H.355, A:A.357, A:E.366, A:E.366

1 x CA: CALCIUM ION(Non-covalent)

CA.4: 6 residues within 4Å: Chain A: N.142, H.168, E.183, D.196, H.231, V.232 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.183, A:D.196, A:H.231, H2O.4, H2O.6

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

GLC.5: 9 residues within 4Å: Chain A: H.101, Y.103, W.104, G.188, L.194, H.317, D.361, R.365 Ligands: P9Q.6 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:W.104, A:D.361, A:R.365, A:R.365 Water bridges: A:H.101, A:H.101

1 x P9Q: (1~{S},2~{R},3~{R},4~{R},5~{R})-5-(8-azanyloctylamino)-4-(hydroxymethyl)cyclohexane-1,2,3-triol(Covalent)

P9Q.6: 15 residues within 4Å: Chain A: Y.103, H.143, L.187, L.194, R.225, D.227, T.228, E.251, L.253, Y.273, H.317, D.318, N.319, R.365 Ligands: GLC.5 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:D.227, A:L.253 Hydrogen bonds: A:R.225, A:R.225, A:T.228, A:H.317, A:D.318, A:R.365 Water bridges: A:E.251, A:E.251

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chen, Y. et al., Activity-Based Protein Profiling of Retaining alpha-Amylases in Complex Biological Samples. J.Am.Chem.Soc. (2021)

Release Date

2021-02-24

Peptides

Alpha-amylase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
AAA

Alpha-amylase

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