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The crystal structure of novel mammalian lectin YM1 suggests a saccharide binding site

Analyse The crystal structure of novel mammalian lectin YM1 suggests a saccharide… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1E9L
Type: protein
Length: 372 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: YM1 secretory protein
UniProt: O35744
Ligands: GCS
Pockets: 1 · best druggability 0.64

Structure

x-ray diffraction · 1 distinct chain · 37% helix, 22% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	YM1 secretory protein	protein	372	37% helix, 22% strand	O35744

Ligands and binding sites

GCS · 2-amino-2-deoxy-beta-D-glucopyranose · sugar · chains A

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

Pockets

1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	445	0.64	0.77	47	GCS

Modifications

Observed in the structure: 2 disulfide, 1 glycan (disulfide, glycosylation).

Compared structures

1E9L · The crystal structure of novel mammalian lectin Ym1 suggests a saccharide binding site · the same entry in another collection · chain A against A, TM-score 1.00
O35744 · AlphaFold monomer V2.0 prediction for chitinase-like protein 3 (O35744) · 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 O35744
Elsewhere: RCSB PDB 1E9L · PDBe 1E9L · UniProt O35744

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