Research workbench

E. COLI (lacz) beta-galactosidase (G794A)

Analyse E. COLI (lacz) beta-galactosidase (G794A) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1PX3
Type: protein
Length: 4,034 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 0.81

Structure

x-ray diffraction · 4 distinct chains · 14% helix, 41% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Beta-galactosidase (EC 3.2.1.23)	protein	1010	14% helix, 41% strand	P00722
B	Beta-galactosidase (EC 3.2.1.23)	protein	1009	14% helix, 41% strand	P00722
C	Beta-galactosidase (EC 3.2.1.23)	protein	1007	14% helix, 41% strand	P00722
D	Beta-galactosidase (EC 3.2.1.23)	protein	1008	14% helix, 41% strand	P00722

Ligands and binding sites

NA · Sodium ion · metal · 16 copies · chains A, B, C, D
MG · Magnesium ion · metal · 12 copies · chains A, B, C, D
DMS · Dimethyl sulfoxide · additive · 85 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	662	0.81	0.86	93	empty
2	928	0.81	0.83	115	empty
3	732	0.79	0.83	99	DMS
4	547	0.75	0.83	67	empty
5	520	0.73	0.82	66	DMS

Interfaces

6 interfaces between chains.

A–D · 2394 Å² buried · 34 hydrogen bonds · protein-protein
B–C · 2335 Å² buried · 33 hydrogen bonds · protein-protein
A–B · 2039 Å² buried · 32 hydrogen bonds · protein-protein
C–D · 2029 Å² buried · 34 hydrogen bonds · protein-protein
B–D · 136 Å² buried · 5 hydrogen bonds · protein-protein

Compared structures

1PX3 · E. COLI (lacz) beta-galactosidase (G794A) · 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 1PX3 · PDBe 1PX3 · UniProt P00722

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