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Structure of the beta-galactosidase from kluyveromyces lactis

Analyse Structure of the beta-galactosidase from kluyveromyces lactis in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3OBA
Type: protein
Length: 4,096 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Beta-galactosidase
EC: 3.2.1.23
UniProt: P00723
Ligands: MN3
Pockets: 20 · best druggability 0.85

Structure

x-ray diffraction · 1 distinct chain · 15% helix, 39% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C, D, B	Beta-galactosidase (EC 3.2.1.23)	protein	1024	15% helix, 39% strand	P00723

Ligands and binding sites

MN3 · Manganese (III) ion · metal · 4 copies · chains A, C, D, B
GOL · Glycerol · additive · 10 copies · chains A, C, D, B

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	947	0.85	0.86	91	empty
2	924	0.85	0.86	87	empty
3	949	0.82	0.84	119	empty
4	971	0.81	0.82	82	empty
5	437	0.78	0.86	54	empty

Interfaces

5 interfaces between chains.

A–B · 2671 Å² buried · 48 hydrogen bonds · protein-protein
A–C · 2638 Å² buried · 39 hydrogen bonds · protein-protein
D–B · 2630 Å² buried · 40 hydrogen bonds · protein-protein
A–D · 402 Å² buried · 6 hydrogen bonds · protein-protein
C–B · 377 Å² buried · 4 hydrogen bonds · protein-protein

Compared structures

3OBA · Structure of the beta-galactosidase from Kluyveromyces lactis · the same entry in another collection · chain B against B, TM-score 1.00
P00723 · AlphaFold monomer V2.0 prediction for beta-galactosidase (P00723) · 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 P00723
Elsewhere: RCSB PDB 3OBA · PDBe 3OBA · UniProt P00723

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