Research workbench
High resolution crystal structure of wheat germ agglutinin in complex with N-acetyl-D-glucosamine
Analyse High resolution crystal structure of wheat germ agglutinin in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2UVO
- Type
- protein
- Length
- 683 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Agglutinin isolectin 1
- UniProt
- P10968
- Ligands
- NDG, NAG
- Pockets
- 8 · best druggability 0.63
Structure
x-ray diffraction · 2 distinct chains · 18% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Agglutinin isolectin 1 | protein | 170 | 18% helix, 23% strand | P10968 |
| B, E, F | Agglutinin isolectin 1 | protein | 171 | 18% helix, 22% strand | P10968 |
Ligands and binding sites
- NDG · 2-acetamido-2-deoxy-alpha-D-glucopyranose · sugar · 9 copies · chains A, B, E, F
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 9 copies · chains A, B, E, F
- GOL · Glycerol · additive · 4 copies · chains A, B, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 76 | 0.63 | 0.91 | 18 | GOL |
| 2 | 82 | 0.62 | 0.90 | 25 | GOL |
| 3 | 128 | 0.62 | 0.86 | 39 | NDG |
| 4 | 83 | 0.60 | 0.89 | 19 | GOL |
| 5 | 76 | 0.60 | 0.89 | 20 | GOL |
Interfaces
2 interfaces between chains.
- A–B · 2385 Ų buried · 50 hydrogen bonds · protein-protein
- E–F · 2377 Ų buried · 49 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 64 disulfide, 4 modified (disulfide, cyclization).
Compared structures
- 2UVO · High Resolution Crystal Structure of Wheat Germ Agglutinin in Complex with… · the same entry in another collection · chain F against F, TM-score 1.00
- P10968 · AlphaFold monomer V2.0 prediction for agglutinin isolectin 1 (P10968) · a predicted model of the same protein · 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 P10968
- Elsewhere: RCSB PDB 2UVO · PDBe 2UVO · UniProt P10968
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