Research workbench
Crystal structure of Ribonuclease A in complex with 5b
Analyse Crystal structure of Ribonuclease A in complex with 5b in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4G8Y
- Type
- protein
- Length
- 248 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.8
- Source
- Bos taurus
- Molecule
- Ribonuclease pancreatic
- EC
- 3.1.27.5
- UniProt
- P61823
- Ligands
- 0FT
- Pockets
- 2 · best druggability 0.36
Structure
x-ray diffraction · resolution 1.8 · 1 distinct chain · 21% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Ribonuclease pancreatic (EC 3.1.27.5) | protein | 124 | 21% helix, 35% strand | P61823 |
Ligands and binding sites
- 0FT · 1-{[1-(alpha-L-arabinofuranosyl)-1H-1,2,3-triazol-4-yl]methyl}-5-methyl-2,4-dioxo-1,2,3,4-tetrahydropyrimidine · ligand · chains A
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 | 84 | 0.36 | 0.76 | 16 | empty |
| 2 | 62 | 0.36 | 0.78 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 324 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 4G8Y · Crystal structure of ribonuclease a in complex with 5B · the same entry in another collection · 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 P61823
- Elsewhere: RCSB PDB 4G8Y · PDBe 4G8Y · UniProt P61823
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