Research workbench

Pea lectin-sucrose complex

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

PDB: 1OFS
Type: protein
Length: 458 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Pea lectin alpha chain; Pea lectin beta chain
UniProt: P02867
Ligands: GLC, FRU, MN, CA
Pockets: 2 · best druggability 0.40

Structure

x-ray diffraction · 2 distinct chains · 4% helix, 48% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	Pea lectin alpha chain	protein	181	3% helix, 45% strand	P02867
B, D	Pea lectin beta chain	protein	48	6% helix, 63% strand	P02867

Ligands and binding sites

GLC · alpha-D-glucopyranose · sugar · 2 copies · chains A, B, C, D
FRU · beta-D-fructofuranose · sugar · 2 copies · chains A, B, C, D
MN · Manganese (II) ion · metal · 2 copies · chains A, C
CA · Calcium ion · metal · 2 copies · chains A, C

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

Pockets

2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	98	0.40	0.77	21	empty
2	71	0.39	0.79	15	empty

Interfaces

5 interfaces between chains.

A–B · 3885 Å² buried · 98 hydrogen bonds · protein-protein
C–D · 3874 Å² buried · 96 hydrogen bonds · protein-protein
A–C · 838 Å² buried · 18 hydrogen bonds · protein-protein
A–D · 158 Å² buried · 1 hydrogen bond · protein-protein
B–C · 146 Å² buried · 1 hydrogen bond · protein-protein

Compared structures

1OFS · Pea lectin-sucrose complex · the same entry in another collection · chain A against A, TM-score 1.00
P02867 · AlphaFold monomer V2.0 prediction for lectin (P02867) · a predicted model of the same protein · chain A against A, TM-score 0.99

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 P02867
Elsewhere: RCSB PDB 1OFS · PDBe 1OFS · UniProt P02867

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.