Research workbench
Deamidated derivative of bovine pancreatic ribonuclease
Analyse Deamidated derivative of bovine pancreatic ribonuclease in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1DY5
- Type
- protein
- Length
- 248 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 0.87
- Source
- BOS TAURUS
- Molecule
- Ribonuclease a
- EC
- 3.1.27.5
- UniProt
- P61823
- Ligands
- SO4
- Pockets
- 2 · best druggability 0.43
Structure
x-ray diffraction · resolution 0.87 · 1 distinct chain · 21% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Ribonuclease a (EC 3.1.27.5) | protein | 124 | 21% helix, 36% strand | P61823 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 3 copies · chains A, B
- IPA · Isopropyl alcohol · additive · 8 copies · chains A, B
- ACT · Acetate ion · additive · 4 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, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 147 | 0.43 | 0.76 | 22 | empty |
| 2 | 55 | 0.26 | 0.73 | 18 | ACT |
Interfaces
1 interface between chains.
- A–B · 287 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 2 modified (disulfide, nonstandard).
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 P61823
- Elsewhere: RCSB PDB 1DY5 · PDBe 1DY5 · UniProt P61823
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