MolNFT v1 · #11416 · protein

Agglutinin in complex with T-disaccharide

1JLX: “Agglutinin in complex with T-disaccharide”. X-ray diffraction, 4 ligands (FOR, MBN, A2G), 4 pockets (best druggability 0.76). MolNFT v1 #11416 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1JLX
Type: protein
Length: 598 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Agglutinin
Ligands: FOR, MBN, A2G, GAL
Pockets: 4 · best druggability 0.76

Structure

x-ray diffraction · 1 distinct chain · 7% helix, 44% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Agglutinin	protein	299	7% helix, 44% strand	—

Ligands and binding sites

FOR · Formyl group · ligand · 2 copies · chains A, B
MBN · Toluene · ligand · 2 copies · chains A, B
A2G · 2-acetamido-2-deoxy-alpha-D-galactopyranose · sugar · 2 copies · chains A, B
GAL · beta-D-galactopyranose · sugar · 2 copies · chains A, B

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	88	0.76	0.97	23	empty
2	83	0.73	0.96	23	empty
3	73	0.32	0.75	16	empty
4	66	0.32	0.75	17	empty

Interfaces

1 interface between chains.

A–B · 2280 Å² buried · 40 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 covalent (covalent ligand).

Compared structures

1JLX · Agglutinin in complex with T-disaccharide · the same entry in another collection · chain A against A, TM-score 1.00

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Elsewhere: RCSB PDB 1JLX · PDBe 1JLX

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