MolNFT v1 · #34925 · protein

Crystal structure of peanut lectin gal-alpha-1,3-gal complex

2DVD · Galactose-binding lectin: “Crystal structure of peanut lectin gal-alpha-1,3-gal complex”. X-ray diffraction, 4 ligands (GAL, CA, MN), 6 pockets (best druggability 0.77). MolNFT v1 #34925 on GenesisL1: 3D structure, binding sites and…

PDB: 2DVD
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, CA, MN, SO4
Pockets: 6 · best druggability 0.77

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 · 8 copies · chains A, B, C, 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 · 4 copies · chains A, B, C, D

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	858	0.77	0.81	110	empty
2	174	0.47	0.76	30	empty
3	126	0.45	0.77	26	empty
4	134	0.44	0.77	26	empty
5	147	0.44	0.76	27	empty

Interfaces

6 interfaces between chains.

A–D · 965 Å² buried · 12 hydrogen bonds · protein-protein
B–C · 965 Å² buried · 13 hydrogen bonds · protein-protein
A–B · 669 Å² buried · 4 hydrogen bonds · protein-protein
C–D · 548 Å² buried · 11 hydrogen bonds · protein-protein
B–D · 66 Å² buried · 2 hydrogen bonds · protein-protein

Compared structures

2DVD · Crystal structure of peanut lectin GAL-ALPHA-1,3-GAL complex · the same entry in another collection · chain C against C, 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 2DVD · PDBe 2DVD · UniProt P02872

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