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The crystal structure of glycosidase mutant

Analyse The crystal structure of glycosidase mutant in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6M6M
Type: protein
Length: 893 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Beta-glucosidase
EC: 3.2.1.21
UniProt: D2PL27
Pockets: 7 · best druggability 0.71

Structure

x-ray diffraction · 2 distinct chains · 43% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Beta-glucosidase (EC 3.2.1.21)	protein	447	43% helix, 16% strand	D2PL27
B	Beta-glucosidase (EC 3.2.1.21)	protein	446	42% helix, 16% strand	D2PL27

Ligands and binding sites

TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · 2 copies · chains A, B

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

Pockets

7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	424	0.71	0.82	46	TRS
2	376	0.69	0.82	47	TRS
3	231	0.62	0.81	42	empty
4	160	0.55	0.81	30	empty
5	117	0.54	0.83	19	empty

Interfaces

1 interface between chains.

A–B · 606 Å² buried · 7 hydrogen bonds · protein-protein

Compared structures

6M6M · The crystal structure of glycosidase mutant · 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
Every structure of UniProt D2PL27
Elsewhere: RCSB PDB 6M6M · PDBe 6M6M · UniProt D2PL27

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