MolNFT v1 · #123484 · protein
The X-ray structure of the adduct formed in the reaction between bovine pancreatic ribonuclease and compound I, a piano-stool organometallic RU(II) arene compound containing an O,S-chelating ligand
5JLG · Ribonuclease pancreatic: “The X-ray structure of the adduct formed in the reaction between bovine pancreatic ribonuclease and compound…”. X-ray diffraction, 2 ligands (6L6, RU), 1 pocket (best druggability 0.49). MolNFT v1 #123484…
- PDB
- 5JLG
- 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
- 6L6, RU
- Pockets
- 1 · best druggability 0.49
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
- 6L6 · methyl (2Z)-3-hydroxy-3-(3-hydroxyphenyl)prop-2-ene(dithioate) · ligand · 2 copies · chains A, B
- RU · Ruthenium ion · metal · 2 copies · chains A, B
- DMS · Dimethyl sulfoxide · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 167 | 0.49 | 0.77 | 29 | empty |
Interfaces
1 interface between chains.
- A–B · 376 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 5JLG · The X-ray structure of the adduct formed in the reaction between bovine pancreatic… · 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 5JLG · PDBe 5JLG · UniProt P61823
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