Research workbench

Peanut lectin

Analyse Peanut lectin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2PEL
Type: protein
Length: 928 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Peanut lectin
UniProt: P02872
Ligands: GAL, GLC, BGC, CA, MN
Pockets: 6 · best druggability 0.76

Structure

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

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

Ligands and binding sites

GAL · beta-D-galactopyranose · sugar · 4 copies · chains A, B, C, D
GLC · alpha-D-glucopyranose · sugar · 3 copies · chains A, B, D
BGC · beta-D-glucopyranose · sugar · chains C
CA · Calcium ion · metal · 4 copies · chains A, B, C, D
MN · Manganese (II) 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

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	1194	0.76	0.79	121	empty
2	131	0.43	0.76	26	empty
3	133	0.42	0.75	22	empty
4	112	0.39	0.75	21	empty
5	95	0.36	0.75	20	empty

Interfaces

6 interfaces between chains.

B–C · 961 Å² buried · 9 hydrogen bonds · protein-protein
A–D · 957 Å² buried · 9 hydrogen bonds · protein-protein
A–B · 679 Å² buried · 5 hydrogen bonds · protein-protein
C–D · 615 Å² buried · 12 hydrogen bonds · protein-protein
A–C · 62 Å² buried · 2 hydrogen bonds · protein-protein

Compared structures

2PEL · Peanut lectin · the same entry in another collection · chain D against D, 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 2PEL · PDBe 2PEL · UniProt P02872

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