MolNFT v1 · #124888 · protein
HMIRO1 C-domain GDP complex C2221 crystal form
5KSP · Mitochondrial rho GTPase 1: “HMIRO1 C-domain GDP complex C2221 crystal form”. X-ray diffraction, 2 ligands (GDP, CL), 4 pockets (best druggability 0.49). MolNFT v1 #124888 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 5KSP
- Type
- protein
- Length
- 315 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mitochondrial rho GTPase 1
- EC
- 3.6.5.-
- UniProt
- Q8IXI2
- Ligands
- GDP, CL
- Pockets
- 4 · best druggability 0.49
Structure
x-ray diffraction · 2 distinct chains · 27% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Mitochondrial rho GTPase 1 (EC 3.6.5.-) | protein | 160 | 28% helix, 25% strand | Q8IXI2 |
| B | Mitochondrial rho GTPase 1 (EC 3.6.5.-) | protein | 155 | 26% helix, 26% strand | Q8IXI2 |
Ligands and binding sites
- GDP · Guanosine-5'-diphosphate · ligand · 2 copies · chains A, B
- CL · Chloride ion · ion · 2 copies · chains A, B
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 | 204 | 0.49 | 0.76 | 35 | GDP, CL |
| 2 | 117 | 0.42 | 0.76 | 21 | empty |
| 3 | 107 | 0.41 | 0.76 | 28 | GDP, CL |
| 4 | 81 | 0.38 | 0.77 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 564 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
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 Q8IXI2
- Elsewhere: RCSB PDB 5KSP · PDBe 5KSP · UniProt Q8IXI2
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