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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: 6SD0
Type: protein
Length: 4,332 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Beta-galactosidase
EC: 3.2.1.23
UniProt: Q56307
Ligands: MG
Pockets: 20 · best druggability 0.86

Structure

x-ray diffraction · 1 distinct chain · 13% helix, 43% strand (DSSP).

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

Ligands and binding sites

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, 13 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1152	0.86	0.87	122	empty
2	353	0.75	0.86	50	empty
3	324	0.74	0.86	50	empty
4	335	0.73	0.85	50	empty
5	70	0.73	0.98	21	empty

Interfaces

3 interfaces between chains.

A–B · 887 Å² buried · 13 hydrogen bonds · protein-protein
B–D · 181 Å² buried · 5 hydrogen bonds · protein-protein
A–C · 165 Å² buried · 4 hydrogen bonds · protein-protein

Compared structures

6SD0 · Structure of beta-galactosidase from Thermotoga maritima. · the same entry in another collection · chain D against D, TM-score 1.00
Q56307 · AlphaFold monomer V2.0 prediction for beta-galactosidase (Q56307) · a predicted model of the same protein · chain A 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 6SD0 · PDBe 6SD0 · UniProt Q56307

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