MolNFT v1 · #11452 · protein
The crystal structure of ribonuclease a in complex with 2'- deoxyuridine 3'-pyrophosphate (P'-5') adenosine
1JN4 · Pancreatic ribonuclease a: “The crystal structure of ribonuclease a in complex with 2'- deoxyuridine 3'-pyrophosphate (P'-5') adenosine”. X-ray diffraction, 1 ligand (139), 2 pockets (best druggability 0.44). MolNFT v1 #11452 on…
- PDB
- 1JN4
- Type
- protein
- Length
- 248 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pancreatic ribonuclease a
- EC
- 3.1.27.5
- UniProt
- P61823
- Ligands
- 139
- Pockets
- 2 · best druggability 0.44
Structure
x-ray diffraction · 1 distinct chain · 21% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Pancreatic ribonuclease a (EC 3.1.27.5) | protein | 124 | 21% helix, 35% strand | P61823 |
Ligands and binding sites
- 139 · Adenosine-5'-[trihydrogen diphosphate] P'-3'-ester with 2'-deoxyuridine · 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 | 126 | 0.44 | 0.77 | 20 | empty |
| 2 | 52 | 0.32 | 0.77 | 15 | 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
- 1JN4 · The Crystal Structure of Ribonuclease A in complex with 2'-deoxyuridine 3'-pyrophosphate… · 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 1JN4 · PDBe 1JN4 · UniProt P61823
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