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Family 89 glycoside hydrolase from clostridium perfringens in complex with 2-acetamido-1,2-dideoxynojirmycin

Analyse Family 89 glycoside hydrolase from clostridium perfringens in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2VC9
Type: protein
Length: 883 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Alpha-N-acetylglucosaminidase
EC: 3.2.1.50
UniProt: Q0TST1
Ligands: NOK, CA
Pockets: 7 · best druggability 0.73

Structure

x-ray diffraction · 1 distinct chain · 41% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Alpha-N-acetylglucosaminidase (EC 3.2.1.50)	protein	883	41% helix, 17% strand	Q0TST1

Ligands and binding sites

NOK · 2-acetamido-1,2-dideoxynojirmycin · ligand · chains A
CA · Calcium ion · metal · 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, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	467	0.73	0.83	62	empty
2	259	0.67	0.83	28	empty
3	231	0.61	0.81	35	empty
4	118	0.61	0.86	22	NOK, GOL
5	138	0.50	0.79	22	empty

Compared structures

2VC9 · Family 89 Glycoside Hydrolase from Clostridium perfringens in complex with… · 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 Q0TST1
Elsewhere: RCSB PDB 2VC9 · PDBe 2VC9 · UniProt Q0TST1

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