Research workbench
Crystal structure of the human MIRO1 N-terminal GTPase bound to GTP
Analyse Crystal structure of the human MIRO1 N-terminal GTPase bound to GTP in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6D71
- Type
- protein
- Length
- 341 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
- GTP, MG
- Pockets
- 7 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Mitochondrial rho GTPase 1 (EC 3.6.5.-) | protein | 172 | 37% helix, 22% strand | Q8IXI2 |
| B | Mitochondrial rho GTPase 1 (EC 3.6.5.-) | protein | 169 | 38% helix, 21% strand | Q8IXI2 |
Ligands and binding sites
- GTP · Guanosine-5'-triphosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 162 | 0.69 | 0.89 | 28 | empty |
| 2 | 97 | 0.56 | 0.86 | 30 | empty |
| 3 | 158 | 0.53 | 0.79 | 23 | empty |
| 4 | 152 | 0.46 | 0.77 | 28 | GTP, MG |
| 5 | 134 | 0.45 | 0.77 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 1300 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
- 6D71 · Crystal Structure of the Human Miro1 N-terminal GTPase bound to GTP · the same entry in another collection · chain A against A, TM-score 1.00
- Q8IXI2 · AlphaFold monomer V2.0 prediction for mitochondrial rho GTPase 1 (Q8IXI2) · a predicted model of the same protein · chain B against A, TM-score 0.97
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 6D71 · PDBe 6D71 · UniProt Q8IXI2
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