MolNFT v1 · #124963 · protein
HMIRO2 C-terminal GTPase domain, GDP-bound
5KUT · Mitochondrial rho GTPase 2: “HMIRO2 C-terminal GTPase domain, GDP-bound”. X-ray diffraction, 2 ligands (GDP, MG), 5 pockets (best druggability 0.81). MolNFT v1 #124963 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5KUT
- Type
- protein
- Length
- 512 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mitochondrial rho GTPase 2
- EC
- 3.6.5.-
- UniProt
- Q8IXI1
- Ligands
- GDP, MG
- Pockets
- 5 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 25% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Mitochondrial rho GTPase 2 (EC 3.6.5.-) | protein | 179 | 25% helix, 23% strand | Q8IXI1 |
| B | Mitochondrial rho GTPase 2 (EC 3.6.5.-) | protein | 170 | 25% helix, 25% strand | Q8IXI1 |
| C | Mitochondrial rho GTPase 2 (EC 3.6.5.-) | protein | 163 | 26% helix, 26% strand | Q8IXI1 |
Ligands and binding sites
- GDP · Guanosine-5'-diphosphate · ligand · 3 copies · chains A, B, C
- MG · Magnesium ion · metal · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 933 | 0.81 | 0.83 | 108 | MG |
| 2 | 76 | 0.37 | 0.77 | 17 | empty |
| 3 | 82 | 0.36 | 0.76 | 24 | empty |
| 4 | 71 | 0.35 | 0.76 | 23 | empty |
| 5 | 76 | 0.32 | 0.74 | 26 | empty |
Interfaces
3 interfaces between chains.
- B–C · 768 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 369 Ų buried · 3 hydrogen bonds · protein-protein
- A–B · 284 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
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 Q8IXI1
- Elsewhere: RCSB PDB 5KUT · PDBe 5KUT · UniProt Q8IXI1
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