MolNFT v1 · #16494 · protein
Ribonuclease a in complex with uridine-2'-phosphate
1O0M · Ribonuclease pancreatic: “Ribonuclease a in complex with uridine-2'-phosphate”. X-ray diffraction, 1 ligand (U2P), 3 pockets (best druggability 0.40). MolNFT v1 #16494 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1O0M
- 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
- U2P
- Pockets
- 3 · best druggability 0.40
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
- U2P · Phosphoric acid mono-[2-(2,4-dioxo-3,4-dihydro-2H-pyrimidin-1-yl)-4-hydroxy-5-hydroxymethyl-tetrahydro-furan-3-yl] ester · ligand · 2 copies · chains A, B
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 | 105 | 0.40 | 0.76 | 20 | empty |
| 2 | 57 | 0.34 | 0.78 | 16 | empty |
| 3 | 58 | 0.34 | 0.77 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 391 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 1O0M · Ribonuclease A in complex with uridine-2'-phosphate · 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 1O0M · PDBe 1O0M · UniProt P61823
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