MolNFT v1 · #53779 · protein
Crystal structure of wheat germ agglutinin isolectin 3 in complex with a synthetic divalent carbohydrate ligand
2X52: “Crystal structure of wheat germ agglutinin isolectin 3 in complex with a synthetic divalent carbohydrate…”. X-ray diffraction, 1 ligand (GYT), 3 pockets (best druggability 0.61). MolNFT v1 #53779 on GenesisL1: 3D structure, binding…
- PDB
- 2X52
- Type
- protein
- Length
- 341 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Agglutinin isolectin 3
- UniProt
- P10969
- Ligands
- GYT
- Pockets
- 3 · best druggability 0.61
Structure
x-ray diffraction · 2 distinct chains · 21% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Agglutinin isolectin 3 | protein | 171 | 18% helix, 21% strand | P10969 |
| B | Agglutinin isolectin 3 | protein | 170 | 24% helix, 22% strand | P10969 |
Ligands and binding sites
- GYT · Bis-(2-acetamido-2-deoxy-alpha-D-glucopyranosyloxycarbonyl)-4,7,10-trioxa-1,13-tridecanediamine · ligand · 4 copies · chains A, B
- GOL · Glycerol · additive · 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 87 | 0.61 | 0.89 | 20 | GOL |
| 2 | 104 | 0.60 | 0.87 | 22 | empty |
| 3 | 82 | 0.51 | 0.84 | 32 | empty |
Interfaces
1 interface between chains.
- A–B · 2310 Ų buried · 48 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 32 disulfide, 1 modified (disulfide, cyclization).
Compared structures
- 2X52 · Crystal structure of wheat germ agglutinin isolectin 3 in complex with a synthetic… · the same entry in another collection · chain A against A, TM-score 1.00
- P10969 · AlphaFold monomer V2.0 prediction for agglutinin isolectin 3 (P10969) · 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 P10969
- Elsewhere: RCSB PDB 2X52 · PDBe 2X52 · UniProt P10969
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