Research workbench
The ribonuclease a- 5'-deoxy-5'-N-pyrrolidinouridine complex
Analyse The ribonuclease a- 5'-deoxy-5'-N-pyrrolidinouridine complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3D7B
- Type
- protein
- Length
- 248 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribonuclease pancreatic
- EC
- 3.1.27.5
- UniProt
- P61823
- Ligands
- U4S
- Pockets
- 3 · best druggability 0.37
Structure
x-ray diffraction · 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
- U4S · 1-(5-deoxy-5-pyrrolidin-1-yl-alpha-L-arabinofuranosyl)pyrimidine-2,4(1H,3H)-dione · ligand · chains A
- FLC · Citrate anion · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 76 | 0.37 | 0.77 | 18 | empty |
| 2 | 77 | 0.35 | 0.76 | 20 | empty |
| 3 | 52 | 0.32 | 0.77 | 11 | empty |
Interfaces
1 interface between chains.
- A–B · 353 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 3D7B · The Ribonuclease A- 5'-Deoxy-5'-N-pyrrolidinouridine complex · 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 3D7B · PDBe 3D7B · UniProt P61823
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