MolNFT v1 · #164851 · protein

Structure of a beta galactosidase with inhibitor

6TBG · Beta-galactosidase, putative, BGL35A: “Structure of a beta galactosidase with inhibitor”. X-ray diffraction, 2 ligands (N0N, NA), 20 pockets (best druggability 0.70). MolNFT v1 #164851 on GenesisL1: 3D structure, binding sites and…

PDB: 6TBG
Type: protein
Length: 4,307 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Beta-galactosidase, putative, BGL35A
EC: 3.2.1.23
UniProt: B3PBE0
Ligands: N0N, NA
Pockets: 20 · best druggability 0.70

Structure

x-ray diffraction · 6 distinct chains · 34% helix, 29% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Beta-galactosidase, putative, BGL35A (EC 3.2.1.23)	protein	535	34% helix, 29% strand	B3PBE0
B, E, G	Beta-galactosidase, putative, BGL35A (EC 3.2.1.23)	protein	540	34% helix, 29% strand	B3PBE0
C	Beta-galactosidase, putative, BGL35A (EC 3.2.1.23)	protein	537	33% helix, 30% strand	B3PBE0
D	Beta-galactosidase, putative, BGL35A (EC 3.2.1.23)	protein	539	35% helix, 29% strand	B3PBE0
F	Beta-galactosidase, putative, BGL35A (EC 3.2.1.23)	protein	539	35% helix, 29% strand	B3PBE0
H	Beta-galactosidase, putative, BGL35A (EC 3.2.1.23)	protein	537	34% helix, 29% strand	B3PBE0

Ligands and binding sites

N0N · 5-(dimethylamino)-~{N}-[6-[[(1~{R},2~{R},3~{S},4~{S}, 5~{S})-2-(hydroxymethyl)-3,4,5-tris(oxidanyl) cyclopentyl]amino]hexyl]naphthalene-1-sulfonamide · ligand · 8 copies · chains A, C, B, H, D, E, G, F
NA · Sodium ion · metal · 30 copies · chains A, B, C, D, E, F, G, H
ACT · Acetate ion · additive · 18 copies · chains A, B, H, C, D, E, G, F

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

Pockets

20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	515	0.70	0.80	61	N0N
2	563	0.68	0.78	62	N0N
3	543	0.68	0.78	61	N0N
4	527	0.67	0.78	50	N0N
5	502	0.67	0.78	60	N0N

Interfaces

9 interfaces between chains.

B–H · 1365 Å² buried · 25 hydrogen bonds · protein-protein
C–H · 1356 Å² buried · 25 hydrogen bonds · protein-protein
F–G · 1351 Å² buried · 23 hydrogen bonds · protein-protein
A–B · 1344 Å² buried · 23 hydrogen bonds · protein-protein
A–C · 1344 Å² buried · 22 hydrogen bonds · protein-protein

Compared structures

6TBG · Structure of a beta galactosidase with inhibitor · 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 B3PBE0
Elsewhere: RCSB PDB 6TBG · PDBe 6TBG · UniProt B3PBE0

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