Research workbench

E. COLI (lacz) beta-galactosidase (N460T)

Analyse E. COLI (lacz) beta-galactosidase (N460T) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3VDA
Type: protein
Length: 4,060 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Beta-galactosidase
EC: 3.2.1.23
UniProt: P00722
Ligands: NA, MG
Pockets: 20 · best druggability 0.80

Structure

x-ray diffraction · 1 distinct chain · 14% helix, 40% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Beta-galactosidase (EC 3.2.1.23)	protein	1015	14% helix, 40% strand	P00722

Ligands and binding sites

NA · Sodium ion · metal · 10 copies · chains A, B, C, D
MG · Magnesium ion · metal · 8 copies · chains A, B, C, D
DMS · Dimethyl sulfoxide · additive · 32 copies · chains A, D, B, 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	892	0.80	0.83	99	empty
2	775	0.79	0.83	105	DMS
3	607	0.76	0.83	69	empty
4	1175	0.75	0.78	103	DMS
5	1147	0.75	0.78	100	empty

Interfaces

6 interfaces between chains.

A–D · 2540 Å² buried · 32 hydrogen bonds · protein-protein
B–C · 2499 Å² buried · 29 hydrogen bonds · protein-protein
A–B · 2092 Å² buried · 23 hydrogen bonds · protein-protein
C–D · 2048 Å² buried · 20 hydrogen bonds · protein-protein
A–C · 143 Å² buried · 4 hydrogen bonds · protein-protein

Compared structures

3VDA · E. coli (lacZ) beta-galactosidase (N460T) · the same entry in another collection · chain D against D, TM-score 1.00
P00722 · AlphaFold monomer V2.0 prediction for beta-galactosidase (P00722) · a predicted model of the same protein · chain D 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 P00722
Elsewhere: RCSB PDB 3VDA · PDBe 3VDA · UniProt P00722

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.