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Crystal structure of exo-1,5-alpha-L-arabinofuranosidase complexed with alpha-1,5-L-arabinofuranobiose

Analyse Crystal structure of exo-1,5-alpha-L-arabinofuranosidase complexed with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3AKG
Type: protein
Length: 447 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Putative secreted alpha L-arabinofuranosidase II
EC: 3.2.1.55
UniProt: Q82P90
Ligands: AHR, NA, CL
Pockets: 5 · best druggability 0.64

Structure

x-ray diffraction · 1 distinct chain · 7% helix, 49% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Putative secreted alpha L-arabinofuranosidase II (EC 3.2.1.55)	protein	447	7% helix, 49% strand	Q82P90

Ligands and binding sites

AHR · alpha-L-arabinofuranose · sugar · 4 copies · chains A
NA · Sodium ion · metal · chains A
CL · Chloride ion · ion · chains A
GOL · Glycerol · additive · 2 copies · chains A

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

Pockets

5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	163	0.64	0.85	23	AHR, GOL
2	263	0.55	0.76	24	empty
3	84	0.50	0.83	23	empty
4	102	0.39	0.76	21	empty
5	97	0.34	0.73	22	empty

Compared structures

3AKG · Crystal structure of exo-1,5-alpha-L-arabinofuranosidase complexed with… · the same entry in another collection · chain A against A, TM-score 1.00
Q82P90 · AlphaFold monomer V2.0 prediction for extracellular exo… · a predicted model of the same protein · chain A against A, TM-score 0.99

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 Q82P90
Elsewhere: RCSB PDB 3AKG · PDBe 3AKG · UniProt Q82P90

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