MolNFT v1 · #191381 · protein

Structure of glycosylated lag-3 homodimer

8DGG · Lymphocyte activation gene 3 protein: “Structure of glycosylated lag-3 homodimer”. X-ray diffraction, 2 ligands (NAG, FUC), 8 pockets (best druggability 0.52). MolNFT v1 #191381 on GenesisL1: 3D structure, binding sites and pockets…

PDB: 8DGG
Type: protein
Length: 631 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Lymphocyte activation gene 3 protein
UniProt: Q61790
Ligands: NAG, FUC
Pockets: 8 · best druggability 0.52

Structure

x-ray diffraction · 2 distinct chains · 3% helix, 37% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Lymphocyte activation gene 3 protein	protein	354	1% helix, 42% strand	Q61790
B	Lymphocyte activation gene 3 protein	protein	277	5% helix, 31% strand	Q61790

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 12 copies · chains A, B
FUC · alpha-L-fucopyranose · sugar · chains A

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

Pockets

8 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	100	0.52	0.82	26	empty
2	140	0.47	0.77	22	empty
3	107	0.42	0.77	23	empty
4	91	0.36	0.75	23	empty
5	60	0.36	0.78	16	empty

Interfaces

1 interface between chains.

A–B · 670 Å² buried · 7 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 7 disulfide, 7 glycan (disulfide, N-glycosylation).

Compared structures

8DGG · Structure of glycosylated LAG-3 homodimer · the same entry in another collection · chain A against A, TM-score 1.00
Q61790 · AlphaFold monomer V2.0 prediction for lymphocyte activation gene 3 protein (Q61790) · a predicted model of the same protein · chain B against A, TM-score 0.72

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 Q61790
Elsewhere: RCSB PDB 8DGG · PDBe 8DGG · UniProt Q61790

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