MolNFT v1 · #13532 · protein

Refinement of two crystal forms of lentil lectin at 1.8 ångströms resolution

1LEN: “Refinement of two crystal forms of lentil lectin at 1.8 ångströms resolution”. X-ray diffraction, 3 ligands (MN, CA, PO4), 2 pockets (best druggability 0.36). MolNFT v1 #13532 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 1LEN
Type: protein
Length: 456 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Lectin
UniProt: P02870
Ligands: MN, CA, PO4
Pockets: 2 · best druggability 0.36

Structure

x-ray diffraction · 2 distinct chains · 3% helix, 51% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	Lectin	protein	181	2% helix, 48% strand	P02870
B, D	Lectin	protein	47	9% helix, 64% strand	P02870

Ligands and binding sites

MN · Manganese (II) ion · metal · 2 copies · chains A, C
CA · Calcium ion · metal · 2 copies · chains A, C
PO4 · Phosphate ion · ion · 2 copies · chains A, B, C, D

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	80	0.36	0.76	18	empty
2	53	0.30	0.76	17	empty

Interfaces

5 interfaces between chains.

A–B · 3890 Å² buried · 87 hydrogen bonds · protein-protein
C–D · 3856 Å² buried · 90 hydrogen bonds · protein-protein
A–C · 830 Å² buried · 15 hydrogen bonds · protein-protein
A–D · 119 Å² buried · 1 hydrogen bond · protein-protein
B–C · 116 Å² buried · 1 hydrogen bond · protein-protein

Compared structures

1LEN · Refinement of two crystal forms of lentil lectin at 1.8 ångströms resolution · 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 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 P02870
Elsewhere: RCSB PDB 1LEN · PDBe 1LEN · UniProt P02870

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