MolNFT v1 · #121707 · protein

Sulfolobus solfataricus beta-glycosidase - E387Y mutant

5I3D · Beta-galactosidase: “Sulfolobus solfataricus beta-glycosidase - E387Y mutant”. X-ray diffraction, 9 pockets (best druggability 0.77). MolNFT v1 #121707 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5I3D
Type: protein
Length: 1,928 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Beta-galactosidase
EC: 3.2.1.23
UniProt: P22498
Pockets: 9 · best druggability 0.77

Structure

x-ray diffraction · 2 distinct chains · 42% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Beta-galactosidase (EC 3.2.1.23)	protein	487	41% helix, 17% strand	P22498
C, D	Beta-galactosidase (EC 3.2.1.23)	protein	477	43% helix, 17% strand	P22498

Ligands and binding sites

ACT · Acetate ion · additive · 15 copies · chains A, B, C, D
PE8 · 3,6,9,12,15,18,21-heptaoxatricosane-1,23-diol · additive · chains A

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

9 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	982	0.77	0.80	92	empty
2	91	0.77	0.98	22	empty
3	97	0.77	0.97	22	empty
4	978	0.72	0.76	85	ACT
5	864	0.71	0.76	72	ACT

Interfaces

4 interfaces between chains.

B–D · 952 Å² buried · 10 hydrogen bonds · protein-protein
A–C · 940 Å² buried · 10 hydrogen bonds · protein-protein
A–B · 525 Å² buried · 10 hydrogen bonds · protein-protein
C–D · 53 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

5I3D · Sulfolobus solfataricus beta-glycosidase - E387Y mutant · the same entry in another collection · chain D against D, TM-score 1.00
P22498 · AlphaFold monomer V2.0 prediction for beta-galactosidase (P22498) · a predicted model of the same protein · chain D against A, TM-score 0.99

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 P22498
Elsewhere: RCSB PDB 5I3D · PDBe 5I3D · UniProt P22498

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