MolNFT v1 · #120864 · protein

Crystal structure of a bacterial fucosidase with iminocyclitol (2S,3S, 4R,5S)-3,4-dihydroxy-2-ethynyl-5-methylpyrrolidine

5HDR · Alpha-L-fucosidase: “Crystal structure of a bacterial fucosidase with iminocyclitol (2S,3S…”. X-ray diffraction, 2 ligands (H79, SO4), 8 pockets (best druggability 0.69). MolNFT v1 #120864 on GenesisL1: 3D structure, binding sites…

PDB: 5HDR
Type: protein
Length: 1,761 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Alpha-L-fucosidase
UniProt: Q8A3I4
Ligands: H79, SO4
Pockets: 8 · best druggability 0.69

Structure

x-ray diffraction · 2 distinct chains · 32% helix, 22% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, D	Alpha-L-fucosidase	protein	440	32% helix, 22% strand	Q8A3I4
C	Alpha-L-fucosidase	protein	441	32% helix, 22% strand	Q8A3I4

Ligands and binding sites

H79 · [(1,2,3,4,5-eta)-cyclopentadienyl][(1,2,3,4,5-eta)-1-{3-[4-(3,4-dihydroxy-5-methylpyrrolidin-2-yl)-1H-1,2,3-triazol-1-yl]prop-1-en-1-yl}cyclopentadienyl]iron · ligand · 4 copies · chains A, B, C, D
SO4 · Sulfate ion · ion · 5 copies · chains A, B, C
IMD · Imidazole · additive · 4 copies · chains A, B, C, D

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

Pockets

8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	827	0.69	0.75	74	empty
2	557	0.66	0.77	56	empty
3	464	0.61	0.76	49	empty
4	116	0.56	0.84	18	empty
5	62	0.42	0.81	18	SO4, H79

Interfaces

3 interfaces between chains.

A–B · 355 Å² buried · 1 hydrogen bond · protein-protein
C–D · 339 Å² buried · 2 hydrogen bonds · protein-protein
B–C · 101 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

5HDR · Crystal structure of a bacterial fucosidase with iminocyclitol… · 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 5HDR · PDBe 5HDR · UniProt Q8A3I4

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