MolNFT v1 · #151851 · protein

Crystal structure of a bacterial fucosidase with inhibitor fucpug

6HZY · Alpha-L-fucosidase: “Crystal structure of a bacterial fucosidase with inhibitor fucpug”. X-ray diffraction, 2 ligands (GYZ, SO4), 5 pockets (best druggability 0.83). MolNFT v1 #151851 on GenesisL1: 3D structure, binding sites and…

PDB: 6HZY
Type: protein
Length: 875 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Alpha-L-fucosidase
UniProt: Q8A3I4
Ligands: GYZ, SO4
Pockets: 5 · best druggability 0.83

Structure

x-ray diffraction · 2 distinct chains · 32% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Alpha-L-fucosidase	protein	438	31% helix, 24% strand	Q8A3I4
B	Alpha-L-fucosidase	protein	437	32% helix, 22% strand	Q8A3I4

Ligands and binding sites

GYZ · [(~{Z})-[(3~{S},4~{R},5~{S},6~{S})-6-methyl-3,4,5-tris(oxidanyl)oxan-2-ylidene]amino] ~{N}-phenylcarbamate · ligand · 2 copies · chains A, B
SO4 · Sulfate ion · ion · 7 copies · chains A, B
EDO · 1,2-ethanediol · additive · 17 copies · chains A, B

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1168	0.83	0.84	97	EDO, SO4
2	62	0.46	0.83	16	GYZ
3	78	0.41	0.79	17	GYZ
4	61	0.27	0.73	18	empty
5	50	0.27	0.74	15	empty

Interfaces

1 interface between chains.

A–B · 1208 Å² buried · 15 hydrogen bonds · protein-protein

Compared structures

6HZY · Crystal structure of a bacterial fucosidase with inhibitor FucPUG · 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 Q8A3I4
Elsewhere: RCSB PDB 6HZY · PDBe 6HZY · UniProt Q8A3I4

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