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Complex of a C. perfringens O-glcnacase with a fragment hit

Analyse Complex of a C. perfringens O-glcnacase with a fragment hit in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5OXD
Type: protein
Length: 580 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: O-glcnacase nagj
EC: 3.2.1.169, 3.2.1.52
UniProt: Q0TR53
Ligands: B2W, CD
Pockets: 6 · best druggability 0.53

Structure

x-ray diffraction · 1 distinct chain · 46% helix, 15% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	O-glcnacase nagj (EC 3.2.1.169, 3.2.1.52)	protein	580	46% helix, 15% strand	Q0TR53

Ligands and binding sites

B2W · 5-(trifluoromethyl)-2,3-dihydro-1~{H}-1,4-diazepine · ligand · chains A
CD · Cadmium ion · metal · 22 copies · chains A

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

Pockets

6 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	104	0.53	0.83	19	CD
2	144	0.41	0.74	14	empty
3	140	0.41	0.74	22	CD
4	72	0.36	0.77	17	empty
5	56	0.36	0.79	16	empty

Compared structures

Q0TR53 · AlphaFold monomer V2.0 prediction for O-glcnacase nagj (Q0TR53) · a predicted model of the same protein · chain A against A, TM-score 0.99

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 Q0TR53
Elsewhere: RCSB PDB 5OXD · PDBe 5OXD · UniProt Q0TR53

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