SMTL ID : 5oss.1

Beta-glucosidase from Thermotoga maritima in complex with Gluco-1H-imidazole

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-dimer

Ligands

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

EDO.1: 4 residues within 4Å: Chain A: V.75, A.76, Y.432, Y.443 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:A.76, A:A.76 Water bridges: A:V.75 EDO.2: 4 residues within 4Å: Chain A: A.166, E.167, R.170, V.229 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.170 EDO.3: 4 residues within 4Å: Chain A: T.112, L.150, K.153, W.164 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.112 EDO.4: 5 residues within 4Å: Chain A: G.65, N.66, V.67, K.68, A.429 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.65, A:E.430 EDO.5: 5 residues within 4Å: Chain A: V.261, R.262, H.265, W.355, K.359 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.359 Water bridges: A:R.262 EDO.6: 5 residues within 4Å: Chain A: L.198, Y.199, F.267, F.289, A.330 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.199 EDO.7: 7 residues within 4Å: Chain A: Q.42, Y.317, W.346, W.420, E.427, W.428, F.436 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.42, A:Q.42 Water bridges: A:N.425 EDO.9: 5 residues within 4Å: Chain B: V.75, A.76, Y.432, Y.443, Q.446 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.446 Water bridges: B:A.76 EDO.10: 5 residues within 4Å: Chain B: R.159, R.221, R.225, D.301, E.304 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:R.159, B:R.221, B:R.225, B:D.301, B:D.301 EDO.11: 3 residues within 4Å: Chain B: Y.199, F.267, P.329 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Y.199

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

CL.8: 2 residues within 4Å: Chain A: N.158, R.159 Ligand excluded by PLIP

1 x NA: SODIUM ION(Non-functional Binders)

NA.12: 3 residues within 4Å: Chain B: D.300, S.303, E.304 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.304

1 x AEZ: (4~{S},5~{S},6~{R},7~{R})-7-(hydroxymethyl)-4,5,6,7-tetrahydro-1~{H}-benzimidazole-4,5,6-triol(Non-covalent)

AEZ.13: 13 residues within 4Å: Chain B: Q.42, H.143, W.144, N.187, E.188, N.315, Y.317, W.346, E.373, W.420, E.427, W.428, F.436 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:Q.42, B:Q.42, B:H.143, B:N.187, B:N.315, B:E.427 Water bridges: B:N.425

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Schroder, S.P. et al., Gluco-1 H-imidazole: A New Class of Azole-Type beta-Glucosidase Inhibitor. J. Am. Chem. Soc. (2018)

Release Date

2018-04-11

Peptides

Beta-glucosidase A: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Beta-glucosidase A

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