Research workbench
X-ray structure of the adduct of a vanadium picolinate complex with RNase a at pH 5.1
Analyse X-ray structure of the adduct of a vanadium picolinate complex with RNase a at… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7P8R
- Type
- protein
- Length
- 241 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribonuclease pancreatic
- EC
- 4.6.1.18
- UniProt
- P61823
- Ligands
- AIV, SO4
- Pockets
- 2 · best druggability 0.36
Structure
x-ray diffraction · 2 distinct chains · 22% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ribonuclease pancreatic (EC 4.6.1.18) | protein | 122 | 21% helix, 36% strand | P61823 |
| B | Ribonuclease pancreatic (EC 4.6.1.18) | protein | 119 | 22% helix, 37% strand | P61823 |
Ligands and binding sites
- AIV · Hydroxy(oxo)bis(pyridine-2-carboxylato-kappa~2~n,o) vanadium(3+) · ligand · chains A
- SO4 · Sulfate ion · ion · 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 | 62 | 0.36 | 0.78 | 13 | empty |
| 2 | 54 | 0.26 | 0.74 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 344 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 7P8R · X-ray structure of the adduct of a vanadium picolinate complex with RNase A at pH 5.1 · 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 7P8R · PDBe 7P8R · UniProt P61823
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