MolNFT v1 · #165358 · protein

Beta-galactosidase in complex with deoxygalacto-nojirimycin

6TSH: “Beta-galactosidase in complex with deoxygalacto-nojirimycin”. Electron microscopy, 2 ligands (DGJ, MG), 20 pockets (best druggability 0.80). MolNFT v1 #165358 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6TSH
Type: protein
Length: 4,060 residues
Chains: 4
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Beta-galactosidase
EC: 3.2.1.23
UniProt: Q8VNN2
Ligands: DGJ, MG
Pockets: 20 · best druggability 0.80

Structure

electron microscopy · 1 distinct chain · 14% helix, 41% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Beta-galactosidase (EC 3.2.1.23)	protein	1015	14% helix, 41% strand	Q8VNN2

Ligands and binding sites

DGJ · (2R,3S,4R,5S)-2-(hydroxymethyl)piperidine-3,4,5-triol · ligand · 4 copies · chains A, B, C, D
MG · Magnesium ion · metal · 4 copies · chains A, B, C, D

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	882	0.80	0.83	107	empty
2	816	0.79	0.82	94	empty
3	625	0.77	0.83	81	empty
4	597	0.76	0.83	77	empty
5	1082	0.76	0.78	103	empty

Interfaces

6 interfaces between chains.

A–D · 2452 Å² buried · 23 hydrogen bonds · protein-protein
B–C · 2448 Å² buried · 23 hydrogen bonds · protein-protein
C–D · 1981 Å² buried · 20 hydrogen bonds · protein-protein
A–B · 1981 Å² buried · 20 hydrogen bonds · protein-protein
B–D · 101 Å² buried · 3 hydrogen bonds · protein-protein

Compared structures

6TSH · Beta-galactosidase in complex with deoxygalacto-nojirimycin · the same entry in another collection · chain D against D, TM-score 1.00
Q8VNN2 · AlphaFold monomer V2.0 prediction for beta-galactosidase (Q8VNN2) · a predicted model of the same protein · chain C 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 Q8VNN2
Elsewhere: RCSB PDB 6TSH · PDBe 6TSH · UniProt Q8VNN2

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