Research workbench

Beta-galactosidase in complex with petg

Analyse Beta-galactosidase in complex with petg in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6TTE
Type: protein
Length: 4,056 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: PTQ, MG
Pockets: 20 · best druggability 0.82

Structure

electron microscopy · 1 distinct chain · 13% helix, 40% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Beta-galactosidase (EC 3.2.1.23)	protein	1014	13% helix, 40% strand	Q8VNN2

Ligands and binding sites

PTQ · 2-phenylethyl 1-thio-beta-D-galactopyranoside · 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	992	0.82	0.83	119	empty
2	1010	0.81	0.83	126	empty
3	674	0.77	0.83	81	empty
4	858	0.77	0.81	93	empty
5	811	0.77	0.81	89	empty

Interfaces

6 interfaces between chains.

B–C · 2347 Å² buried · 27 hydrogen bonds · protein-protein
A–D · 2346 Å² buried · 27 hydrogen bonds · protein-protein
C–D · 2039 Å² buried · 20 hydrogen bonds · protein-protein
A–B · 2039 Å² buried · 20 hydrogen bonds · protein-protein
A–C · 113 Å² buried · 3 hydrogen bonds · protein-protein

Compared structures

6TTE · Beta-galactosidase in complex with PETG · 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 B 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 6TTE · PDBe 6TTE · UniProt Q8VNN2

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