MolNFT v1 · #1347 · protein

Glycosylasparaginase

1AYY: “Glycosylasparaginase”. X-ray diffraction, 5 pockets (best druggability 0.53). MolNFT v1 #1347 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1AYY
Type: protein
Length: 565 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Glycosylasparaginase
EC: 3.5.1.26
UniProt: Q47898
Pockets: 5 · best druggability 0.53

Structure

x-ray diffraction · 4 distinct chains · 35% helix, 25% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Glycosylasparaginase (EC 3.5.1.26)	protein	138	43% helix, 15% strand	Q47898
B	Glycosylasparaginase (EC 3.5.1.26)	protein	143	27% helix, 34% strand	Q47898
C	Glycosylasparaginase (EC 3.5.1.26)	protein	140	44% helix, 15% strand	Q47898
D	Glycosylasparaginase (EC 3.5.1.26)	protein	144	26% helix, 35% strand	Q47898

Pockets

5 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	59	0.53	0.88	25	empty
2	143	0.46	0.77	30	empty
3	91	0.34	0.74	15	empty
4	83	0.34	0.75	18	empty
5	61	0.27	0.73	11	empty

Interfaces

6 interfaces between chains.

A–B · 2687 Å² buried · 50 hydrogen bonds · protein-protein
C–D · 2646 Å² buried · 46 hydrogen bonds · protein-protein
A–D · 700 Å² buried · 11 hydrogen bonds · protein-protein
B–C · 665 Å² buried · 9 hydrogen bonds · protein-protein
B–D · 645 Å² buried · 6 hydrogen bonds · protein-protein

Compared structures

1AYY · Glycosylasparaginase · the same entry in another collection · chain D against D, TM-score 1.00
Q47898 · AlphaFold monomer V2.0 prediction for N(4)-(beta-N- acetylglucosaminyl)-L-asparaginase… · 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 Q47898
Elsewhere: RCSB PDB 1AYY · PDBe 1AYY · UniProt Q47898

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