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Crystal structure of amaranthus caudatus agglutinin

Analyse Crystal structure of amaranthus caudatus agglutinin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1JLY
Type: protein
Length: 598 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Agglutinin
UniProt: Q71QF2
Ligands: FOR
Pockets: 4 · best druggability 0.76

Structure

x-ray diffraction · 1 distinct chain · 7% helix, 45% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Agglutinin	protein	299	7% helix, 45% strand	Q71QF2

Ligands and binding sites

FOR · Formyl group · ligand · 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	97	0.76	0.97	24	empty
2	80	0.74	0.97	23	empty
3	96	0.35	0.74	20	empty
4	57	0.28	0.74	16	empty

Interfaces

1 interface between chains.

A–B · 2290 Å² buried · 42 hydrogen bonds · protein-protein

Modifications

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

Compared structures

1JLY · Crystal structure of amaranthus caudatus agglutinin · 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
Every structure of UniProt Q71QF2
Elsewhere: RCSB PDB 1JLY · PDBe 1JLY · UniProt Q71QF2

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