MolNFT v2 · #21108 · protein
Agglutinin from Ricinus communis with galactoaza
1RZO: “Agglutinin from Ricinus communis with galactoaza”. X-ray diffraction at 2.63, 2 ligands (GAL, SO4), 12 pockets (best druggability 0.76). MolNFT v2 #21108 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1RZO
- Type
- protein
- Length
- 1,043 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.63
- Source
- Ricinus communis
- Molecule
- Agglutinin
- EC
- 3.2.2.22
- UniProt
- P06750
- Ligands
- GAL, SO4
- Pockets
- 12 · best druggability 0.76
Structure
x-ray diffraction · resolution 2.63 · 3 distinct chains · 30% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Agglutinin (EC 3.2.2.22) | protein | 259 | 42% helix, 23% strand | P06750 |
| B, D | Agglutinin | protein | 262 | 10% helix, 38% strand | P06750 |
| C | Agglutinin (EC 3.2.2.22) | protein | 260 | 40% helix, 23% strand | P06750 |
Ligands and binding sites
- GAL · beta-D-galactopyranose · sugar · 11 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 10 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 150 | 0.76 | 0.93 | 33 | empty |
| 2 | 105 | 0.69 | 0.91 | 33 | empty |
| 3 | 352 | 0.63 | 0.79 | 50 | empty |
| 4 | 276 | 0.58 | 0.78 | 35 | empty |
| 5 | 164 | 0.57 | 0.81 | 32 | empty |
Interfaces
3 interfaces between chains.
- C–D · 1956 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 1927 Ų buried · 21 hydrogen bonds · protein-protein
- A–C · 636 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide (disulfide).
Compared structures
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 P06750
- Elsewhere: RCSB PDB 1RZO · PDBe 1RZO · UniProt P06750
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