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Hydroxynitrile lyase from almond, monoclinic crystal form

Analyse Hydroxynitrile lyase from almond, monoclinic crystal form in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3GDP
Type: protein
Length: 1,042 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: R-oxynitrile lyase isoenzyme 1
EC: 4.1.2.10
UniProt: Q945K2
Ligands: FAD, NAG, MAN, FUC, BMA, FUL, NDG
Pockets: 5 · best druggability 0.85

Structure

x-ray diffraction · 1 distinct chain · 28% helix, 27% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	R-oxynitrile lyase isoenzyme 1 (EC 4.1.2.10)	protein	521	28% helix, 27% strand	Q945K2

Ligands and binding sites

FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains A, B
NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 11 copies · chains A, B
MAN · alpha-D-mannopyranose · sugar · 4 copies · chains A, B
FUC · alpha-L-fucopyranose · sugar · 2 copies
BMA · beta-D-mannopyranose · sugar · 2 copies · chains A
FUL · beta-L-fucopyranose · sugar
NDG · 2-acetamido-2-deoxy-alpha-D-glucopyranose · sugar · chains B
IPA · Isopropyl alcohol · additive · 2 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, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	600	0.85	0.90	91	FAD
2	1069	0.84	0.85	135	FAD
3	165	0.51	0.78	32	IPA
4	168	0.50	0.77	36	IPA, NAG
5	50	0.25	0.73	20	empty

Interfaces

1 interface between chains.

A–B · 460 Å² buried · 3 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 glycan, 2 disulfide (N-glycosylation, disulfide).

Compared structures

3GDP · Hydroxynitrile lyase from almond, monoclinic crystal form · the same entry in another collection · chain A against A, TM-score 1.00
Q945K2 · AlphaFold monomer V2.0 prediction for (R)-mandelonitrile lyase 2 (Q945K2) · a predicted model of the same protein · 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 Q945K2
Elsewhere: RCSB PDB 3GDP · PDBe 3GDP · UniProt Q945K2

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