MolNFT v1 · #26039 · protein

Crystal structure of arabinofuranosidase complexed with arabinose

1WD4 · Alpha-L-arabinofuranosidase B: “Crystal structure of arabinofuranosidase complexed with arabinose”. X-ray diffraction, 2 ligands (AHR, NAG), 2 pockets (best druggability 0.56). MolNFT v1 #26039 on GenesisL1: 3D structure, binding…

PDB: 1WD4
Type: protein
Length: 482 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Alpha-L-arabinofuranosidase B
EC: 3.2.1.55
Ligands: AHR, NAG
Pockets: 2 · best druggability 0.56

Structure

x-ray diffraction · 1 distinct chain · 10% helix, 38% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Alpha-L-arabinofuranosidase B (EC 3.2.1.55)	protein	482	10% helix, 38% strand	—

Ligands and binding sites

AHR · alpha-L-arabinofuranose · sugar · 3 copies · chains A
NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A

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

Pockets

2 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	143	0.56	0.82	27	empty
2	152	0.50	0.79	24	empty

Modifications

Observed in the structure: 4 disulfide, 1 glycan (disulfide, N-glycosylation).

Compared structures

1WD4 · Crystal structure of arabinofuranosidase complexed with arabinose · 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
Elsewhere: RCSB PDB 1WD4 · PDBe 1WD4

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