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E. COLI (lacz) beta-galactosidase (G974A) in complex with allolactose

Analyse E. COLI (lacz) beta-galactosidase (G974A) in complex with allolactose in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4DUW
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: BGC, GAL, NA, MG
Pockets: 20 · best druggability 0.82

Structure

x-ray diffraction · 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	P00722

Ligands and binding sites

BGC · beta-D-glucopyranose · sugar · 4 copies · chains A, D, B, C
GAL · beta-D-galactopyranose · sugar · 4 copies · chains A, B, C, D
NA · Sodium ion · metal · 16 copies · chains A, B, C, D
MG · Magnesium ion · metal · 10 copies · chains A, B, C, D
DMS · Dimethyl sulfoxide · additive · 77 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	1013	0.82	0.83	119	empty
2	1176	0.82	0.83	147	DMS
3	653	0.77	0.83	82	empty
4	1099	0.76	0.79	100	DMS
5	1165	0.76	0.79	108	DMS

Interfaces

6 interfaces between chains.

B–C · 2454 Å² buried · 28 hydrogen bonds · protein-protein
A–D · 2444 Å² buried · 28 hydrogen bonds · protein-protein
A–B · 2043 Å² buried · 29 hydrogen bonds · protein-protein
C–D · 2040 Å² buried · 29 hydrogen bonds · protein-protein
A–C · 159 Å² buried · 5 hydrogen bonds · protein-protein

Compared structures

4DUW · E. coli (lacZ) beta-galactosidase (G974A) in complex with allolactose · 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 4DUW · PDBe 4DUW · UniProt P00722

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