MolNFT v1 · #34928 · protein

Crystal structure of peanut lectin gal-alpha-1,6-glc complex

2DVG · Galactose-binding lectin: “Crystal structure of peanut lectin gal-alpha-1,6-glc complex”. X-ray diffraction, 5 ligands (GLA, BGC, CA), 6 pockets (best druggability 0.77). MolNFT v1 #34928 on GenesisL1: 3D structure, binding sites…

PDB: 2DVG
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: GLA, BGC, CA, MN, SO4
Pockets: 6 · best druggability 0.77

Structure

x-ray diffraction · 1 distinct chain · 4% helix, 49% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Galactose-binding lectin	protein	232	4% helix, 49% strand	P02872

Ligands and binding sites

GLA · alpha-D-galactopyranose · sugar · 4 copies · chains D, A, B, C
BGC · beta-D-glucopyranose · sugar · chains D
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 · 2 copies · chains A, B, C

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

Pockets

6 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	836	0.77	0.81	108	empty
2	189	0.49	0.77	32	empty
3	157	0.47	0.77	32	empty
4	140	0.45	0.76	28	empty
5	88	0.38	0.77	19	empty

Interfaces

6 interfaces between chains.

B–C · 972 Å² buried · 14 hydrogen bonds · protein-protein
A–D · 960 Å² buried · 10 hydrogen bonds · protein-protein
A–B · 681 Å² buried · 2 hydrogen bonds · protein-protein
C–D · 559 Å² buried · 12 hydrogen bonds · protein-protein
B–D · 68 Å² buried · 1 hydrogen bond · protein-protein

Compared structures

2DVG · Crystal structure of peanut lectin GAL-ALPHA-1,6-GLC 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 2DVG · PDBe 2DVG · UniProt P02872

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