MolNFT v1 · #155615 · protein

Structure of bifidobacterium dentium beta-glucuronidase

6LD6 · LACZ1 beta-galactosidase: “Structure of bifidobacterium dentium beta-glucuronidase”. X-ray diffraction, 20 pockets (best druggability 0.90). MolNFT v1 #155615 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6LD6
Type: protein
Length: 2,480 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: LACZ1 beta-galactosidase
EC: 3.2.1.23
UniProt: D2Q7B1
Pockets: 20 · best druggability 0.90

Structure

x-ray diffraction · 1 distinct chain · 21% helix, 35% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	LACZ1 beta-galactosidase (EC 3.2.1.23)	protein	620	21% helix, 35% strand	D2Q7B1

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	1075	0.90	0.93	117	empty
2	213	0.83	0.97	36	empty
3	462	0.82	0.89	56	empty
4	198	0.82	0.96	34	empty
5	360	0.80	0.90	45	empty

Interfaces

6 interfaces between chains.

A–C · 2446 Å² buried · 29 hydrogen bonds · protein-protein
B–D · 2421 Å² buried · 31 hydrogen bonds · protein-protein
B–C · 2294 Å² buried · 18 hydrogen bonds · protein-protein
A–D · 2287 Å² buried · 17 hydrogen bonds · protein-protein
C–D · 597 Å² buried · 11 hydrogen bonds · protein-protein

Compared structures

6LD6 · Structure of Bifidobacterium dentium beta-glucuronidase · 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 D2Q7B1
Elsewhere: RCSB PDB 6LD6 · PDBe 6LD6 · UniProt D2Q7B1

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