MolNFT v1 · #1057 · protein

Human aspartylglucosaminidase

1APY: “Human aspartylglucosaminidase”. X-ray diffraction, 2 ligands (NAG, BMA), 4 pockets (best druggability 0.44). MolNFT v1 #1057 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1APY
Type: protein
Length: 604 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Aspartylglucosaminidase
EC: 3.5.1.26
UniProt: P20933
Ligands: NAG, BMA
Pockets: 4 · best druggability 0.44

Structure

x-ray diffraction · 2 distinct chains · 31% helix, 27% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	Aspartylglucosaminidase (EC 3.5.1.26)	protein	161	39% helix, 17% strand	P20933
B, D	Aspartylglucosaminidase (EC 3.5.1.26)	protein	141	23% helix, 38% strand	P20933

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 5 copies · chains D, A, B, C
BMA · beta-D-mannopyranose · sugar

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

Pockets

4 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	113	0.44	0.78	23	empty
2	110	0.44	0.78	23	empty
3	92	0.42	0.78	16	empty
4	76	0.39	0.78	16	empty

Interfaces

6 interfaces between chains.

C–D · 2846 Å² buried · 48 hydrogen bonds · protein-protein
A–B · 2801 Å² buried · 48 hydrogen bonds · protein-protein
A–C · 1103 Å² buried · 21 hydrogen bonds · protein-protein
B–D · 660 Å² buried · 12 hydrogen bonds · protein-protein
B–C · 627 Å² buried · 10 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 disulfide, 4 glycan (disulfide, N-glycosylation).

Compared structures

1APY · Human aspartylglucosaminidase · the same entry in another collection · chain A against A, TM-score 1.00
P20933 · AlphaFold monomer V2.0 prediction for N(4)-(beta-N- acetylglucosaminyl)-L-asparaginase… · a predicted model of the same protein · chain B 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 P20933
Elsewhere: RCSB PDB 1APY · PDBe 1APY · UniProt P20933

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