MolNFT v1 · #16715 · protein

Human beta-hexosaminidase B

1O7A · Beta-hexosaminidase beta chain: “Human beta-hexosaminidase B”. X-ray diffraction, 2 ligands (GDL, NAG), 20 pockets (best druggability 0.80). MolNFT v1 #16715 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1O7A
Type: protein
Length: 2,897 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Beta-hexosaminidase beta chain
EC: 3.2.1.52
UniProt: P07686
Ligands: GDL, NAG
Pockets: 20 · best druggability 0.80

Structure

x-ray diffraction · 2 distinct chains · 36% helix, 20% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, E, F	Beta-hexosaminidase beta chain (EC 3.2.1.52)	protein	483	36% helix, 20% strand	P07686
D	Beta-hexosaminidase beta chain (EC 3.2.1.52)	protein	482	36% helix, 20% strand	P07686

Ligands and binding sites

GDL · 2-(acetylamido)-2-deoxy-D-glucono-1,5-lactone · ligand · 6 copies · chains A, B, C, D, E, F
NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 18 copies · chains A, B, C, D, E, F
EDO · 1,2-ethanediol · additive · 15 copies · chains A, C, B, E, D, F

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

Pockets

20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	120	0.80	0.98	35	EDO
2	115	0.78	0.97	34	EDO
3	983	0.77	0.79	84	GDL, EDO
4	645	0.73	0.80	73	EDO
5	491	0.71	0.81	58	empty

Interfaces

8 interfaces between chains.

C–D · 1448 Å² buried · 17 hydrogen bonds · protein-protein
A–B · 1437 Å² buried · 18 hydrogen bonds · protein-protein
A–C · 809 Å² buried · 13 hydrogen bonds · protein-protein
B–D · 754 Å² buried · 11 hydrogen bonds · protein-protein
B–C · 483 Å² buried · 7 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 18 disulfide, 12 glycan (disulfide, N-glycosylation).

Compared structures

1O7A · Human beta-Hexosaminidase B · the same entry in another collection · chain F against F, TM-score 1.00
P07686 · AlphaFold monomer V2.0 prediction for beta-hexosaminidase subunit beta (P07686) · a predicted model of the same protein · chain D 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 P07686
Elsewhere: RCSB PDB 1O7A · PDBe 1O7A · UniProt P07686

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