SMTL ID : 8r06.1

CRYSTAL STRUCTURE OF THERMOANAEROBACTERIUM XYLANOLYTICUM GH116 BETA-GLUCOSIDASE WITH A COVALENTLY BOUND CYCLOPHELLITOL AZIRIDINE

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

monomer

Ligands

1 x PO8: (1~{R},2~{S},3~{S},4~{S},5~{R},6~{R})-5-azanyl-6-(hydroxymethyl)cyclohexane-1,2,3,4-tetrol(Covalent)

PO8.1: 15 residues within 4Å: Chain A: E.426, Y.430, Y.432, T.435, D.437, H.492, Y.508, W.516, T.576, D.578, W.717, E.762, R.771, Y.775, R.777 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:E.426, A:Y.430 Hydrogen bonds: A:D.437, A:H.492, A:D.578, A:E.762, A:R.771, A:R.771, A:R.777

1 x CA: CALCIUM ION(Non-covalent)

CA.2: 5 residues within 4Å: Chain A: D.560, D.562, D.564, I.566, D.568 6 PLIP interactions: 5 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.560, A:D.562, A:D.564, A:I.566, A:D.568, H2O.1

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 4 residues within 4Å: Chain A: G.347, K.348, N.349, N.352 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.348, A:N.349, A:N.352 Water bridges: A:N.349 GOL.4: 3 residues within 4Å: Chain A: R.417, T.418, N.419 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.417, A:T.418, A:T.418

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

CL.5: 2 residues within 4Å: Chain A: K.693, Y.742 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lahav, D. et al., CRYSTAL STRUCTURE OF THERMOANAEROBACTERIUM XYLOLYTICUM GH116 BETA-GLUCOSIDASE WITH A COVALENTLY BOUND CYCLOPHELLITOL AZIRIDINE. JACS (2017)

Release Date

2023-11-22

Peptides

Glucosylceramidase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Glucosylceramidase

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