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Crystal structure of thermoanaerobacterium xylolyticum GH116 beta- glucosidase with an covalent inhibitor

Analyse Crystal structure of thermoanaerobacterium xylolyticum GH116 beta- glucosidase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5NCX
Type: protein
Length: 771 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Glucosylceramidase
EC: 3.2.1.45
UniProt: F6BL85
Ligands: K35, CA, CL
Pockets: 7 · best druggability 0.52

Structure

x-ray diffraction · 1 distinct chain · 30% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Glucosylceramidase (EC 3.2.1.45)	protein	771	30% helix, 23% strand	F6BL85

Ligands and binding sites

K35 · ~{N}-[(1~{R},2~{R},3~{R},4~{S},5~{S},6~{S})-2-(hydroxymethyl)-3,4,5,6-tetrakis(oxidanyl) cyclohexyl]pentanamide · ligand · chains A
CA · Calcium ion · metal · chains A
CL · Chloride ion · ion · chains A
GOL · Glycerol · additive · 2 copies · chains A

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

7 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	144	0.52	0.80	26	K35
2	137	0.44	0.76	23	empty
3	82	0.36	0.76	21	empty
4	58	0.34	0.77	12	empty
5	70	0.31	0.74	15	empty

Modifications

Observed in the structure: 1 covalent (covalent ligand).

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Every structure of UniProt F6BL85
Elsewhere: RCSB PDB 5NCX · PDBe 5NCX · UniProt F6BL85

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