MolNFT v1 · #48776 · protein

Agglutinin from abrus precatorius (apa-I)

2Q3N · Agglutinin-1 a chain: “Agglutinin from abrus precatorius (apa-I)”. X-ray diffraction, 1 ligand (NAG), 5 pockets (best druggability 0.69). MolNFT v1 #48776 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 2Q3N
Type: protein
Length: 508 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Agglutinin-1 a chain; Agglutinin-1 B chain
EC: 3.2.2.22
UniProt: Q9M6E9
Ligands: NAG
Pockets: 5 · best druggability 0.69

Structure

x-ray diffraction · 2 distinct chains · 24% helix, 30% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Agglutinin-1 a chain (EC 3.2.2.22)	protein	247	40% helix, 21% strand	Q9M6E9
B	Agglutinin-1 B chain	protein	261	8% helix, 39% strand	Q9M6E9

Ligands and binding sites

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

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

Pockets

5 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	179	0.69	0.88	29	empty
2	183	0.51	0.77	30	empty
3	120	0.50	0.80	29	empty
4	135	0.48	0.78	17	empty
5	57	0.46	0.84	23	empty

Interfaces

1 interface between chains.

A–B · 1739 Å² buried · 13 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 5 disulfide (disulfide).

Compared structures

2Q3N · Agglutinin from Abrus Precatorius (APA-I) · the same entry in another collection · chain A against A, 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 2Q3N · PDBe 2Q3N · UniProt Q9M6E9

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