MolNFT v1 · #139292 · protein

GH42 alpha-L-arabinopyranosidase from bifidobacterium animalis subsp. lactis bl-04

5XB7 · Beta-galactosidase: “GH42 alpha-L-arabinopyranosidase from bifidobacterium animalis subsp. lactis bl-04”. X-ray diffraction, 1 ligand (SO4), 20 pockets (best druggability 0.71). MolNFT v1 #139292 on GenesisL1: 3D structure, binding…

PDB: 5XB7
Type: protein
Length: 4,119 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Beta-galactosidase
UniProt: A0A1M2TTS0
Ligands: SO4
Pockets: 20 · best druggability 0.71

Structure

x-ray diffraction · 6 distinct chains · 34% helix, 22% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Beta-galactosidase	protein	685	34% helix, 21% strand	A0A1M2TTS0
B	Beta-galactosidase	protein	685	34% helix, 22% strand	A0A1M2TTS0
C	Beta-galactosidase	protein	682	34% helix, 22% strand	A0A1M2TTS0
D	Beta-galactosidase	protein	685	34% helix, 21% strand	A0A1M2TTS0
E	Beta-galactosidase	protein	684	33% helix, 21% strand	A0A1M2TTS0
F	Beta-galactosidase	protein	698	33% helix, 22% strand	A0A1M2TTS0

Ligands and binding sites

SO4 · Sulfate ion · ion · 16 copies · chains A, B, D, C, E, F
GOL · Glycerol · additive · 55 copies · chains A, D, C, B, F, E

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	54	0.71	0.99	19	empty
2	58	0.71	0.98	20	empty
3	51	0.70	0.98	20	empty
4	52	0.69	0.97	19	empty
5	813	0.69	0.75	80	SO4

Interfaces

12 interfaces between chains.

C–D · 2443 Å² buried · 39 hydrogen bonds · protein-protein
A–C · 2430 Å² buried · 40 hydrogen bonds · protein-protein
A–D · 2426 Å² buried · 41 hydrogen bonds · protein-protein
B–F · 2410 Å² buried · 40 hydrogen bonds · protein-protein
E–F · 2407 Å² buried · 39 hydrogen bonds · protein-protein

Compared structures

5XB7 · GH42 alpha-L-arabinopyranosidase from Bifidobacterium animalis subsp. lactis Bl-04 · the same entry in another collection · chain A 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 A0A1M2TTS0
Elsewhere: RCSB PDB 5XB7 · PDBe 5XB7 · UniProt A0A1M2TTS0

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.