Research workbench

Peanut lectin complexed with methyl-beta-galactose

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

PDB: 1QF3
Type: protein
Length: 928 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Protein (peanut lectin)
UniProt: P02872
Ligands: MBG, CA, MN
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	Protein (peanut lectin)	protein	232	4% helix, 50% strand	P02872

Ligands and binding sites

MBG · methyl beta-D-galactopyranoside · ligand · 4 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

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	1135	0.76	0.79	123	empty
2	124	0.43	0.76	25	empty
3	136	0.42	0.75	24	empty
4	109	0.40	0.76	20	empty
5	98	0.38	0.76	19	empty

Interfaces

6 interfaces between chains.

A–D · 970 Å² buried · 12 hydrogen bonds · protein-protein
B–C · 964 Å² buried · 13 hydrogen bonds · protein-protein
A–B · 624 Å² buried · 2 hydrogen bonds · protein-protein
C–D · 580 Å² buried · 8 hydrogen bonds · protein-protein
B–D · 59 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

1QF3 · Peanut lectin complexed with methyl-beta-galactose · 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 1QF3 · PDBe 1QF3 · UniProt P02872

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