SMTL ID : 6yqc.2 (1 other biounit)

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.35 Å

Oligo State

monomer

Ligands

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

EDO.1: 8 residues within 4Å: Chain A: L.187, D.227, T.228, K.230, H.231, E.251, L.253 Ligands: QJN.12 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.231, A:E.251 Water bridges: A:L.253 EDO.2: 5 residues within 4Å: Chain A: S.302, D.303, C.304, P.305 Ligands: EDO.7 No protein-ligand interaction detected (PLIP) EDO.3: 7 residues within 4Å: Chain A: K.284, S.285, T.286, S.287, T.326, D.328, L.331 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.286 Water bridges: A:T.286, A:T.286 EDO.5: 6 residues within 4Å: Chain A: T.94, A.95, Y.96, D.147, G.148, T.191 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.95, A:T.191 EDO.6: 5 residues within 4Å: Chain A: Y.356, A.357, G.358, E.366 Ligands: EDO.9 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.357, A:G.358 EDO.7: 6 residues within 4Å: Chain A: P.257, A.258, C.261, P.262, D.303 Ligands: EDO.2 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.258 Water bridges: A:D.303 EDO.8: 10 residues within 4Å: Chain A: V.86, T.87, I.108, Y.109, S.110, L.111, W.211, L.215, Y.219 Ligands: NAG.4 No protein-ligand interaction detected (PLIP) EDO.9: 5 residues within 4Å: Chain A: Y.356, E.366, L.370, S.371 Ligands: EDO.6 No protein-ligand interaction detected (PLIP) EDO.10: 5 residues within 4Å: Chain A: D.397, G.399, T.402, Y.403, T.421 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.399, A:T.421 EDO.11: 2 residues within 4Å: Chain A: D.154, S.156 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.156, A:S.156

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

NAG.4: 7 residues within 4Å: Chain A: Y.109, W.211, S.214, L.215, N.218, Y.219 Ligands: EDO.8 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.215 Hydrogen bonds: A:S.214, A:N.218

1 x QJN: (1~{R},2~{S},4~{R},5~{S},6~{R})-6-[(2~{S},3~{R},4~{R},5~{S},6~{R})-5-heptoxy-6-(hydroxymethyl)-3,4-bis(oxidanyl)oxan-2-yl]oxy-5-(hydroxymethyl)cyclohexane-1,2,4-triol(Covalent)

QJN.12: 21 residues within 4Å: Chain A: Q.56, Y.96, H.101, Y.103, W.104, V.140, H.143, L.187, G.188, V.192, L.194, R.225, D.227, T.228, E.251, H.317, D.318, D.361, P.362, R.365 Ligands: EDO.1 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:Y.96, A:Y.96, A:D.227 Hydrogen bonds: A:W.104, A:H.143, A:R.225, A:R.225, A:D.227, A:H.317, A:D.318, A:D.361, A:R.365, A:R.365 Water bridges: A:Y.100, A:H.101, A:H.101 Salt bridges: A:H.101

1 x CA: CALCIUM ION(Non-covalent)

CA.13: 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.3, H2O.6

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

2021-02-10

Peptides

Alpha-amylase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
BBB

Alpha-amylase

Related Entries With Identical Sequence