MolNFT v1 · #13535 · protein

Lentil lectin complexed with sucrose

1LES: “Lentil lectin complexed with sucrose”. X-ray diffraction, 4 ligands (GLC, FRU, CA), 2 pockets (best druggability 0.35). MolNFT v1 #13535 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1LES
Type: protein
Length: 456 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Lentil lectin
UniProt: P02870
Ligands: GLC, FRU, CA, MN
Pockets: 2 · best druggability 0.35

Structure

x-ray diffraction · 2 distinct chains · 4% helix, 50% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	Lentil lectin	protein	181	3% helix, 46% strand	—
B, D	Lentil lectin	protein	47	9% helix, 64% strand	P02870

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
CA · Calcium ion · metal · 2 copies · chains A, C
MN · Manganese (II) 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	74	0.35	0.76	19	empty
2	58	0.33	0.77	21	empty

Interfaces

5 interfaces between chains.

A–B · 3893 Å² buried · 102 hydrogen bonds · protein-protein
C–D · 3893 Å² buried · 102 hydrogen bonds · protein-protein
A–C · 859 Å² buried · 20 hydrogen bonds · protein-protein
A–D · 123 Å² buried · 1 hydrogen bond · protein-protein
C–B · 119 Å² buried · 1 hydrogen bond · protein-protein

Compared structures

1LES · Lentil lectin complexed with sucrose · the same entry in another collection · chain A against A, TM-score 1.00
P02870 · AlphaFold monomer V2.0 prediction for lectin (P02870) · a predicted model of the same protein · chain B against A, TM-score 0.98

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 P02870
Elsewhere: RCSB PDB 1LES · PDBe 1LES · UniProt P02870

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