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Crystal structure of peanut lectin gal-beta-1,6-galnac complex

Analyse Crystal structure of peanut lectin gal-beta-1,6-galnac complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2DVB
Type: protein
Length: 928 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Galactose-binding lectin
UniProt: P02872
Ligands: GAL, NGA, CA, MN, SO4
Pockets: 5 · best druggability 0.76

Structure

x-ray diffraction · 1 distinct chain · 4% helix, 50% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Galactose-binding lectin	protein	232	4% helix, 50% strand	P02872

Ligands and binding sites

GAL · beta-D-galactopyranose · sugar · 4 copies · chains A, B, C, D
NGA · 2-acetamido-2-deoxy-beta-D-galactopyranose · sugar · chains A
CA · Calcium ion · metal · 4 copies · chains A, B, C, D
MN · Manganese (II) ion · metal · 4 copies · chains A, B, C, D
SO4 · Sulfate ion · ion · 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	856	0.76	0.80	101	empty
2	178	0.48	0.77	30	empty
3	146	0.46	0.77	30	empty
4	145	0.45	0.77	29	empty
5	121	0.42	0.76	23	empty

Interfaces

6 interfaces between chains.

A–D · 974 Å² buried · 15 hydrogen bonds · protein-protein
B–C · 965 Å² buried · 13 hydrogen bonds · protein-protein
A–B · 706 Å² buried · 4 hydrogen bonds · protein-protein
C–D · 553 Å² buried · 14 hydrogen bonds · protein-protein
B–D · 65 Å² buried · 1 hydrogen bond · protein-protein

Compared structures

2DVB · Crystal structure of peanut lectin GAl-beta-1,6-GalNAc complex · the same entry in another collection · chain A against A, TM-score 1.00
P02872 · AlphaFold monomer V2.0 prediction for galactose-binding lectin (P02872) · 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 P02872
Elsewhere: RCSB PDB 2DVB · PDBe 2DVB · UniProt P02872

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