Research workbench

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

Analyse Refinement of two crystal forms of lentil lectin at 1.8 ångströms resolution in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

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.