Research workbench
X-ray structure of the adduct formed upon reaction of bovine pancreatic ribonuclease with a PD(II) complex bearing N,N- pyridylbenzimidazole derivative with an alkylated sulphonate side chain
Analyse X-ray structure of the adduct formed upon reaction of bovine pancreatic… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6GOK
- 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
- F6Q, PD
- Pockets
- 2 · best druggability 0.44
Structure
x-ray diffraction · 1 distinct chain · 21% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Ribonuclease pancreatic (EC 3.1.27.5) | protein | 124 | 21% helix, 36% strand | P61823 |
Ligands and binding sites
- F6Q · N,N-pyridylbenzimidazole derivative-Pd complex · ligand · 2 copies · chains A, B
- PD · Palladium ion · metal · 2 copies · chains A, B
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 | 165 | 0.44 | 0.75 | 34 | empty |
| 2 | 62 | 0.38 | 0.79 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 334 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 6GOK · X-ray structure of the adduct formed upon reaction of bovine pancreatic ribonuclease with… · 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 6GOK · PDBe 6GOK · UniProt P61823
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