Research workbench

Winged bean lectin complexed with methyl-alpha-D-galactose

Analyse Winged bean lectin complexed with methyl-alpha-D-galactose in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1WBL
Type: protein
Length: 948 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Winged bean lectin
UniProt: O24313
Ligands: AMG, NAG, FUC, MN, CA
Pockets: 5 · best druggability 0.73

Structure

x-ray diffraction · 1 distinct chain · 4% helix, 46% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Winged bean lectin	protein	237	4% helix, 46% strand	O24313

Ligands and binding sites

AMG · methyl alpha-D-galactopyranoside · ligand · 4 copies · chains A, B, C, D
NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 14 copies · chains A, B, C, D
FUC · alpha-L-fucopyranose · sugar · 5 copies · chains C, D
MN · Manganese (II) ion · metal · 4 copies · chains A, B, C, D
CA · Calcium ion · metal · 4 copies · chains A, B, C, D

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

Pockets

5 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	652	0.73	0.80	73	empty
2	102	0.35	0.73	15	empty
3	56	0.32	0.77	17	AMG
4	70	0.32	0.74	15	empty
5	55	0.32	0.77	17	AMG

Interfaces

5 interfaces between chains.

C–D · 853 Å² buried · 10 hydrogen bonds · protein-protein
A–B · 837 Å² buried · 9 hydrogen bonds · protein-protein
B–C · 287 Å² buried · 2 hydrogen bonds · protein-protein
A–D · 275 Å² buried · 6 hydrogen bonds · protein-protein
B–D · 37 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 7 glycan (N-glycosylation).

Compared structures

1WBL · Winged bean lectin complexed with methyl-alpha-D-galactose · the same entry in another collection · chain A against A, TM-score 1.00
O24313 · AlphaFold monomer V2.0 prediction for basic agglutinin (O24313) · 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 O24313
Elsewhere: RCSB PDB 1WBL · PDBe 1WBL · UniProt O24313

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