Research workbench
X-ray structure of the complex between bovine pancreatic ribonuclease and PENTHACHLOROCARBONYLIRIDATE(III) (2 months of soaking)
Analyse X-ray structure of the complex between bovine pancreatic ribonuclease and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5JML
- 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
- IR, CL, CMO, O
- Pockets
- 4 · best druggability 0.38
Structure
x-ray diffraction · 1 distinct chain · 22% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Ribonuclease pancreatic (EC 3.1.27.5) | protein | 124 | 22% helix, 35% strand | P61823 |
Ligands and binding sites
- IR · Iridium ion · metal · 8 copies · chains A, B
- CL · Chloride ion · ion · 5 copies · chains A, B
- CMO · Carbon monoxide · ion · 4 copies · chains A, B
- O · Oxygen atom · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 56 | 0.38 | 0.80 | 14 | empty |
| 2 | 76 | 0.38 | 0.78 | 20 | empty |
| 3 | 60 | 0.33 | 0.77 | 16 | empty |
| 4 | 69 | 0.30 | 0.74 | 19 | IR |
Interfaces
1 interface between chains.
- A–B · 373 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 5JML · X-ray structure of the complex between bovine pancreatic ribonuclease and… · 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 5JML · PDBe 5JML · UniProt P61823
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