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E.COLI (lacz) beta-galactosidase (H418E) in complex with galactose

Analyse E.COLI (lacz) beta-galactosidase (H418E) in complex with galactose in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3E1F
Type: protein
Length: 4,044 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: GAL, NA, MG
Pockets: 20 · best druggability 0.82

Structure

x-ray diffraction · 1 distinct chain · 13% helix, 42% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
1, 2, 3, 4	Beta-galactosidase (EC 3.2.1.23)	protein	1011	13% helix, 42% strand	P00722

Ligands and binding sites

GAL · beta-D-galactopyranose · sugar · 8 copies · chains 1, 2, 3, 4
NA · Sodium ion · metal · 13 copies · chains 1, 2, 3, 4
MG · Magnesium ion · metal · 10 copies · chains 1, 2, 3, 4
DMS · Dimethyl sulfoxide · additive · 73 copies · chains 1, 3, 2, 4

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	1018	0.82	0.83	103	empty
2	1064	0.82	0.83	93	empty
3	762	0.81	0.85	97	empty
4	582	0.79	0.85	86	DMS
5	452	0.73	0.83	44	DMS

Interfaces

6 interfaces between chains.

1–4 · 2107 Å² buried · 30 hydrogen bonds · protein-protein
1–2 · 2073 Å² buried · 24 hydrogen bonds · protein-protein
2–3 · 2070 Å² buried · 27 hydrogen bonds · protein-protein
3–4 · 2066 Å² buried · 23 hydrogen bonds · protein-protein
1–3 · 182 Å² buried · 8 hydrogen bonds · protein-protein

Compared structures

3E1F · E.Coli (lacZ) beta-galactosidase (H418E) in complex with galactose · the same entry in another collection · chain 4 against 4, TM-score 1.00
P00722 · AlphaFold monomer V2.0 prediction for beta-galactosidase (P00722) · a predicted model of the same protein · chain 4 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 3E1F · PDBe 3E1F · UniProt P00722

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