Research workbench

Agglutinin from abrus precatorius

Analyse Agglutinin from abrus precatorius in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2ZR1
Type: protein
Length: 1,026 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Agglutinin-1 chain a; Agglutinin-1 chain B
EC: 3.2.2.22
UniProt: Q9M6E9
Ligands: NAG
Pockets: 8 · best druggability 0.69

Structure

x-ray diffraction · 2 distinct chains · 28% helix, 32% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	Agglutinin-1 chain a (EC 3.2.2.22)	protein	250	44% helix, 26% strand	Q9M6E9
B, D	Agglutinin-1 chain B	protein	263	13% helix, 37% strand	Q9M6E9

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains B, A, C, D

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

Pockets

8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	267	0.69	0.84	57	empty
2	175	0.68	0.87	31	empty
3	207	0.59	0.80	32	empty
4	163	0.52	0.79	22	empty
5	169	0.52	0.78	30	empty

Interfaces

2 interfaces between chains.

A–B · 1842 Å² buried · 22 hydrogen bonds · protein-protein
C–D · 1736 Å² buried · 17 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 10 disulfide, 3 glycan (disulfide, N-glycosylation).

Compared structures

2ZR1 · Agglutinin from Abrus Precatorius · the same entry in another collection · chain D against D, TM-score 1.00
Q9M6E9 · AlphaFold monomer V2.0 prediction for agglutinin-1 (Q9M6E9) · a predicted model of the same protein · chain B 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 Q9M6E9
Elsewhere: RCSB PDB 2ZR1 · PDBe 2ZR1 · UniProt Q9M6E9

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