MolNFT v1 · #78629 · protein

E. COLI (lacz) beta-galactosidase (S796A)

3SEP: “E. COLI (lacz) beta-galactosidase (S796A)”. X-ray diffraction, 2 ligands (NA, MG), 20 pockets (best druggability 0.83). MolNFT v1 #78629 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3SEP
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 0.83

Structure

x-ray diffraction · 1 distinct chain · 14% helix, 41% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Beta-galactosidase (EC 3.2.1.23)	protein	1015	14% helix, 41% strand	P00722

Ligands and binding sites

NA · Sodium ion · metal · 14 copies · chains A, B, C, D
MG · Magnesium ion · metal · 9 copies · chains A, B, C, D
DMS · Dimethyl sulfoxide · additive · 78 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	842	0.83	0.85	121	DMS
2	1067	0.82	0.83	118	empty
3	743	0.79	0.83	82	empty
4	761	0.78	0.83	107	DMS
5	447	0.73	0.83	57	DMS

Interfaces

6 interfaces between chains.

A–D · 2552 Å² buried · 35 hydrogen bonds · protein-protein
B–C · 2466 Å² buried · 31 hydrogen bonds · protein-protein
C–D · 2032 Å² buried · 35 hydrogen bonds · protein-protein
A–B · 2028 Å² buried · 29 hydrogen bonds · protein-protein
A–C · 140 Å² buried · 5 hydrogen bonds · protein-protein

Compared structures

3SEP · E. coli (lacZ) beta-galactosidase (S796A) · 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 3SEP · PDBe 3SEP · UniProt P00722

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