MolNFT v1 · #153357 · protein

Crystal structure of endo-deglycosylated hydroxynitrile lyase isozyme 5 of prunus communis

6JBY · Hnl isoenzyme 5: “Crystal structure of endo-deglycosylated hydroxynitrile lyase isozyme 5 of prunus communis”. X-ray diffraction, 2 ligands (FAD, NAG), 2 pockets (best druggability 0.86). MolNFT v1 #153357 on GenesisL1: 3D…

PDB: 6JBY
Type: protein
Length: 521 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Hnl isoenzyme 5
EC: 4.1.2.10
Ligands: FAD, NAG
Pockets: 2 · best druggability 0.86

Structure

x-ray diffraction · 1 distinct chain · 29% helix, 27% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Hnl isoenzyme 5 (EC 4.1.2.10)	protein	521	29% helix, 27% strand	—

Ligands and binding sites

FAD · Flavin-adenine dinucleotide · ligand · chains A
NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 7 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, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	732	0.86	0.89	101	FAD
2	62	0.34	0.77	17	empty

Modifications

Observed in the structure: 6 glycan, 1 disulfide (N-glycosylation, disulfide).

Compared structures

6JBY · Crystal structure of endo-deglycosylated hydroxynitrile lyase isozyme 5 of Prunus communis · 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 6JBY · PDBe 6JBY

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