Research workbench
Fragment based lead discovery using crystallography
Analyse Fragment based lead discovery using crystallography in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1WBU
- Type
- protein
- Length
- 248 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribonuclease
- EC
- 3.1.27.5
- UniProt
- P61824
- Ligands
- WBU
- Pockets
- 2 · best druggability 0.51
Structure
x-ray diffraction · 1 distinct chain · 21% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Ribonuclease (EC 3.1.27.5) | protein | 124 | 21% helix, 35% strand | P61824 |
Ligands and binding sites
- WBU · 5-amino-1H-pyrimidine-2,4-dione · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 180 | 0.51 | 0.78 | 28 | empty |
| 2 | 62 | 0.34 | 0.77 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 361 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 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 P61824
- Elsewhere: RCSB PDB 1WBU · PDBe 1WBU · UniProt P61824
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