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Crystal structure of urtica dioica agglutinin isolectin VI complex with tri-N-acetylchitotriose

Analyse Crystal structure of urtica dioica agglutinin isolectin VI complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1EHH
Type: protein
Length: 178 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Agglutinin isolectin VI
Ligands: NAG
Pockets: 3 · best druggability 0.39

Structure

x-ray diffraction · 1 distinct chain · 19% helix, 24% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Agglutinin isolectin VI	protein	89	19% helix, 24% strand	—

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains A, B

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

Pockets

3 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	62	0.39	0.80	18	empty
2	71	0.30	0.73	13	NAG
3	55	0.25	0.73	16	empty

Interfaces

1 interface between chains.

A–B · 50 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 16 disulfide, 2 modified (disulfide, cyclization).

Compared structures

1EHH · Crystal structure of urtica dioica agglutinin isolectin VI complex with… · 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 1EHH · PDBe 1EHH

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