Research workbench
Unexpected imidazole coordination to dirhodium tetraacetate complex in a protein environment: insights from X-ray crystallography and quantum chemistry
Analyse Unexpected imidazole coordination to dirhodium tetraacetate complex in a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7QHR
- Type
- protein
- Length
- 248 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
- D1O, D3I, CJI, D5A
- 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 | Ribonuclease pancreatic (EC 4.6.1.18) | protein | 124 | 21% helix, 35% strand | P61823 |
Ligands and binding sites
- D1O · tri-(mi2-acetato-(O, O')-diaqua-dirhodium(II, II) · ligand · 2 copies · chains A, B
- D3I · octaaqua-dirhodium (II, II) fragment · ligand · chains A
- CJI · cis-mi2-acetato-(O, O')-N-imidazyl-pentaaqua-dirhodium(II, II) · ligand · chains A, B
- D5A · trans-mi2-acetato-(O, O')-N-imidazyl-pentaaqua-dirhodium(II, II) · ligand · chains 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 | 154 | 0.44 | 0.76 | 25 | empty |
| 2 | 62 | 0.38 | 0.79 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 327 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 7QHR · Unexpected imidazole coordination to dirhodium tetraacetate complex in a protein… · 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 7QHR · PDBe 7QHR · UniProt P61823
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