SMTL ID : 5n6s.4 (3 other biounits)

Thermotoga maritima family 1 Glycoside hydrolase complexed with Carba-Cyclophellitol transition state mimic

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

monomer

Ligands

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

EDO.1: 7 residues within 4Å: Chain A: S.40, Y.41, E.44, G.45, P.47, G.73, R.106 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:G.45, A:G.73, A:R.106 Water bridges: A:D.145, A:D.145 EDO.2: 4 residues within 4Å: Chain A: H.202, E.427, W.428, A.429 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.202, A:A.429 EDO.3: 4 residues within 4Å: Chain A: V.75, A.76, Y.432, Y.443 1 PLIP interactions: 1 interactions with chain A Water bridges: A:Y.432 EDO.4: 5 residues within 4Å: Chain A: A.157, R.159, R.214, N.218, P.295 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.214, A:N.218

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

CL.5: 2 residues within 4Å: Chain A: N.158, R.159 Ligand excluded by PLIP

1 x 8P5: azanylidene-[4-[[(1~{S},2~{R},3~{R},4~{R},5~{S},6~{S},7~{S})-2-(hydroxymethyl)-3,4,5-tris(oxidanyl)-7-bicyclo[4.1.0]heptanyl]carbonylamino]butylimino]azanium(Non-covalent)

8P5.6: 11 residues within 4Å: Chain A: Q.42, H.143, N.187, E.188, Y.317, W.346, E.373, W.420, E.427, W.428, F.436 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:Y.317 Hydrogen bonds: A:Q.42, A:Q.42, A:N.187, A:E.188, A:N.315, A:E.427 Water bridges: A:E.427

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Beenakker, T.J.M. et al., Carba-cyclophellitols Are Neutral Retaining-Glucosidase Inhibitors. J. Am. Chem. Soc. (2017)

Release Date

2017-03-01

Peptides

Beta-glucosidase A: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

Beta-glucosidase A

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