Research workbench

Structure of beta-galactosidase from thermotoga maritima

Analyse Structure of beta-galactosidase from thermotoga maritima in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6S6Z
Type: protein
Length: 8,664 residues
Chains: 8
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Beta-galactosidase
EC: 3.2.1.23
UniProt: Q56307
Ligands: MG
Pockets: 20 · best druggability 0.80

Structure

electron microscopy · 1 distinct chain · 13% helix, 43% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, D, B, H, F, G, E, C	Beta-galactosidase (EC 3.2.1.23)	protein	1083	13% helix, 43% strand	Q56307

Ligands and binding sites

MG · Magnesium ion · metal · 8 copies · chains A, D, B, H, F, G, E, C

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	446	0.80	0.88	48	empty
2	421	0.78	0.87	44	empty
3	497	0.78	0.85	45	empty
4	393	0.78	0.87	42	empty
5	309	0.78	0.89	31	empty

Interfaces

16 interfaces between chains.

F–E · 2747 Å² buried · 27 hydrogen bonds · protein-protein
H–G · 2746 Å² buried · 27 hydrogen bonds · protein-protein
A–B · 2744 Å² buried · 27 hydrogen bonds · protein-protein
D–C · 2744 Å² buried · 27 hydrogen bonds · protein-protein
G–E · 956 Å² buried · 10 hydrogen bonds · protein-protein

Compared structures

6S6Z · Structure of beta-Galactosidase from Thermotoga maritima · the same entry in another collection · chain C against C, TM-score 1.00
Q56307 · AlphaFold monomer V2.0 prediction for beta-galactosidase (Q56307) · a predicted model of the same protein · chain F 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 Q56307
Elsewhere: RCSB PDB 6S6Z · PDBe 6S6Z · UniProt Q56307

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