MolNFT v1 · #38025 · protein

X-ray crystal structure of ngt-bound hexa

2GK1 · Beta-hexosaminidase subunit alpha: “X-ray crystal structure of ngt-bound hexa”. X-ray diffraction, 3 ligands (NGT, NAG, BMA), 20 pockets (best druggability 0.81). MolNFT v1 #38025 on GenesisL1: 3D structure, binding sites and…

PDB: 2GK1
Type: protein
Length: 3,887 residues
Chains: 20
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Beta-hexosaminidase subunit alpha; Beta-hexosaminidase subunit beta; Beta-hexosaminidase…
EC: 3.2.1.52
UniProt: P06865, P07686
Ligands: NGT, NAG, BMA
Pockets: 20 · best druggability 0.81

Structure

x-ray diffraction · 6 distinct chains · 33% helix, 22% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C, E, G	Beta-hexosaminidase subunit alpha	protein	52	29% helix, 29% strand	P06865
I, J, K, L	Beta-hexosaminidase subunit alpha (EC 3.2.1.52)	protein	440	35% helix, 20% strand	P06865
B, D, F, H	Beta-hexosaminidase subunit beta	protein	54	31% helix, 28% strand	P07686
M, Q, S	Beta-hexosaminidase subunit beta chain B (EC 3.2.1.52)	protein	190	24% helix, 29% strand	P07686
N, P, R, T	Beta-hexosaminidase subunit beta chain a (EC 3.2.1.52)	protein	236	46% helix, 13% strand	P07686
O	Beta-hexosaminidase subunit beta chain B (EC 3.2.1.52)	protein	189	24% helix, 28% strand	P07686

Ligands and binding sites

NGT · 3ar,5r,6s,7r,7ar-5-hydroxymethyl-2-methyl-5,6,7,7A-tetrahydro-3AH-pyrano[3,2-d]thiazole-6,7-diol · ligand · 8 copies · chains I, N, M, J, P, O, K, R, Q, L, S, T
NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 22 copies · chains I, A, B, M, J, C, D, O, E, K, F, Q, L, G, H, S
BMA · beta-D-mannopyranose · sugar · 5 copies

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	154	0.81	0.98	38	empty
2	120	0.79	0.98	33	empty
3	785	0.76	0.80	93	empty
4	1032	0.76	0.78	104	empty
5	1116	0.75	0.77	111	empty

Interfaces

53 interfaces between chains.

S–T · 3347 Å² buried · 51 hydrogen bonds · protein-protein
M–N · 3317 Å² buried · 53 hydrogen bonds · protein-protein
O–P · 3314 Å² buried · 59 hydrogen bonds · protein-protein
Q–R · 3304 Å² buried · 53 hydrogen bonds · protein-protein
G–L · 2638 Å² buried · 40 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 24 disulfide, 9 glycan (disulfide, N-glycosylation).

Compared structures

2GK1 · X-ray crystal structure of NGT-bound HexA · the same entry in another collection · chain P against P, 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 P06865
Every structure of UniProt P07686
Elsewhere: RCSB PDB 2GK1 · PDBe 2GK1 · UniProt P06865 · UniProt P07686

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.