MolNFT v1 · #15247 · protein

Myrosinase from sinapis alba

1MYR: “Myrosinase from sinapis alba”. X-ray diffraction, 7 ligands (NAG, BMA, XYP), 2 pockets (best druggability 0.72). MolNFT v1 #15247 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1MYR
Type: protein
Length: 499 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Myrosinase
EC: 3.2.3.1
UniProt: P29736
Ligands: NAG, BMA, XYP, FUC, MAN, ZN, SO4
Pockets: 2 · best druggability 0.72

Structure

x-ray diffraction · 1 distinct chain · 43% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Myrosinase (EC 3.2.3.1)	protein	499	43% helix, 18% strand	P29736

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 13 copies · chains A
BMA · beta-D-mannopyranose · sugar · 2 copies
XYP · beta-D-xylopyranose · sugar · 2 copies · chains A
FUC · alpha-L-fucopyranose · sugar · 2 copies · chains A
MAN · alpha-D-mannopyranose · sugar · 2 copies · chains A
ZN · Zinc ion · metal · chains A
SO4 · Sulfate ion · ion · 10 copies · chains A
GOL · Glycerol · additive · 4 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	529	0.72	0.81	45	SO4, GOL
2	69	0.30	0.74	20	empty

Modifications

Observed in the structure: 9 glycan, 3 disulfide (N-glycosylation, disulfide).

Compared structures

1MYR · Myrosinase from sinapis alba · the same entry in another collection · chain A against A, TM-score 1.00
P29736 · AlphaFold monomer V2.0 prediction for myrosinase MA1 (P29736) · 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 P29736
Elsewhere: RCSB PDB 1MYR · PDBe 1MYR · UniProt P29736

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