MolNFT v1 · #120061 · protein

The structure of wt BGL6

5GNY · Beta-glucosidase: “The structure of wt BGL6”. X-ray diffraction, 1 ligand (BGC), 20 pockets (best druggability 0.75). MolNFT v1 #120061 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5GNY
Type: protein
Length: 1,792 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Beta-glucosidase
EC: 3.2.1.21
Ligands: BGC
Pockets: 20 · best druggability 0.75

Structure

x-ray diffraction · 2 distinct chains · 44% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Beta-glucosidase (EC 3.2.1.21)	protein	448	44% helix, 16% strand	—
B, C, D	Beta-glucosidase (EC 3.2.1.21)	protein	448	44% helix, 16% strand	—

Ligands and binding sites

BGC · beta-D-glucopyranose · sugar · 4 copies · chains A, B, C, D

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	757	0.75	0.80	74	empty
2	777	0.75	0.79	84	empty
3	557	0.70	0.79	50	BGC
4	558	0.70	0.79	51	BGC
5	508	0.69	0.79	49	BGC

Interfaces

4 interfaces between chains.

C–D · 1063 Å² buried · 14 hydrogen bonds · protein-protein
A–B · 1044 Å² buried · 12 hydrogen bonds · protein-protein
A–C · 580 Å² buried · 4 hydrogen bonds · protein-protein
B–D · 556 Å² buried · 3 hydrogen bonds · protein-protein

Compared structures

5GNY · The structure of WT Bgl6 · the same entry in another collection · chain A against A, TM-score 1.00

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Elsewhere: RCSB PDB 5GNY · PDBe 5GNY

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