Research workbench
Structure of rho guanine nucleotide dissociation inhibitor
Analyse Structure of rho guanine nucleotide dissociation inhibitor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1RHO
- Type
- protein
- Length
- 427 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Rho GDP-dissociation inhibitor 1
- UniProt
- P52565
- Ligands
- SO4
- Pockets
- 6 · best druggability 0.65
Structure
x-ray diffraction · 2 distinct chains · 3% helix, 55% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Rho GDP-dissociation inhibitor 1 | protein | 145 | 3% helix, 53% strand | P52565 |
| C | Rho GDP-dissociation inhibitor 1 | protein | 137 | 3% helix, 56% strand | P52565 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 9 copies · chains A, C, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 293 | 0.65 | 0.81 | 44 | empty |
| 2 | 343 | 0.59 | 0.77 | 39 | empty |
| 3 | 92 | 0.46 | 0.80 | 17 | empty |
| 4 | 101 | 0.46 | 0.79 | 18 | empty |
| 5 | 99 | 0.44 | 0.78 | 17 | empty |
Interfaces
3 interfaces between chains.
- A–C · 549 Ų buried · 11 hydrogen bonds · protein-protein
- B–C · 171 Ų buried · 1 hydrogen bond · protein-protein
- A–B · 93 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 9 modified (engineered).
Compared structures
- 1RHO · Structure of rho guanine nucleotide dissociation inhibitor · the same entry in another collection · chain A against A, TM-score 1.00
- P52565 · AlphaFold monomer V2.0 prediction for rho GDP-dissociation inhibitor 1 (P52565) · a predicted model of the same protein · chain C against A, TM-score 0.98
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 P52565
- Elsewhere: RCSB PDB 1RHO · PDBe 1RHO · UniProt P52565
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