MolNFT v1 · #165360 · protein

Beta-galactosidase in complex with L-ribose

6TSK: “Beta-galactosidase in complex with L-ribose”. Electron microscopy, 2 ligands (0MK, MG), 20 pockets (best druggability 0.80). MolNFT v1 #165360 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6TSK
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: 0MK, MG
Pockets: 20 · best druggability 0.80

Structure

electron microscopy · 1 distinct chain · 13% helix, 41% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Beta-galactosidase (EC 3.2.1.23)	protein	1015	13% helix, 41% strand	Q8VNN2

Ligands and binding sites

0MK · beta-L-ribopyranose · sugar · 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	829	0.80	0.83	97	empty
2	800	0.79	0.83	92	empty
3	910	0.78	0.81	100	empty
4	1168	0.76	0.78	111	empty
5	1089	0.76	0.78	102	empty

Interfaces

6 interfaces between chains.

A–D · 2474 Å² buried · 23 hydrogen bonds · protein-protein
B–C · 2464 Å² buried · 22 hydrogen bonds · protein-protein
C–D · 1970 Å² buried · 23 hydrogen bonds · protein-protein
A–B · 1969 Å² buried · 24 hydrogen bonds · protein-protein
A–C · 106 Å² buried · 1 hydrogen bond · protein-protein

Compared structures

6TSK · Beta-galactosidase in complex with L-ribose · 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 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 Q8VNN2
Elsewhere: RCSB PDB 6TSK · PDBe 6TSK · UniProt Q8VNN2

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