MolNFT v1 · #141319 · protein

Glycosidase F290Y

5Z3D · Glycoside hydrolase 15-related protein: “Glycosidase F290Y”. X-ray diffraction, 2 pockets (best druggability 0.65). MolNFT v1 #141319 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5Z3D
Type: protein
Length: 371 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Glycoside hydrolase 15-related protein
UniProt: D2PPM8
Pockets: 2 · best druggability 0.65

Structure

x-ray diffraction · 1 distinct chain · 57% helix, 5% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Glycoside hydrolase 15-related protein	protein	371	57% helix, 5% strand	D2PPM8

Ligands and binding sites

GOL · Glycerol · additive · 2 copies · chains A
CIT · Citric acid · additive · chains A

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

Pockets

2 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	179	0.65	0.85	23	GOL
2	50	0.26	0.74	16	empty

Modifications

Observed in the structure: 1 modified (oxidation).

Compared structures

5Z3D · Glycosidase F290Y · the same entry in another collection · chain A against A, TM-score 1.00
D2PPM8 · AlphaFold monomer V2.0 prediction for isomaltose glucohydrolase (D2PPM8) · a predicted model of the same protein · 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 D2PPM8
Elsewhere: RCSB PDB 5Z3D · PDBe 5Z3D · UniProt D2PPM8

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