MolNFT v1 · #87414 · protein
Crystal structure of drosophila miro ef hand and cgtpase domains bound to one magnesium ion and MG:GDP (mggdp-miros)
4C0L · Mitochondrial rho GTPase: “Crystal structure of drosophila miro ef hand and cgtpase domains bound to one magnesium ion and MG:GDP…”. X-ray diffraction, 6 ligands (GDP, HSE, MG), 7 pockets (best druggability 0.73). MolNFT v1 #87414…
- PDB
- 4C0L
- Type
- protein
- Length
- 404 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mitochondrial rho GTPase
- EC
- 3.6.5.-
- UniProt
- Q8IMX7
- Ligands
- GDP, HSE, MG, NA, SO4, UNX
- Pockets
- 7 · best druggability 0.73
Structure
x-ray diffraction · 1 distinct chain · 41% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Mitochondrial rho GTPase (EC 3.6.5.-) | protein | 404 | 41% helix, 16% strand | Q8IMX7 |
Ligands and binding sites
- GDP · Guanosine-5'-diphosphate · ligand · chains A
- HSE · L-homoserine · ligand · chains A
- MG · Magnesium ion · metal · 2 copies · chains A
- NA · Sodium ion · metal · chains A
- SO4 · Sulfate ion · ion · 3 copies · chains A
- UNX · Unknown atom or ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 244 | 0.73 | 0.87 | 32 | HSE |
| 2 | 157 | 0.50 | 0.78 | 21 | SO4 |
| 3 | 99 | 0.44 | 0.79 | 18 | empty |
| 4 | 95 | 0.42 | 0.78 | 21 | GDP |
| 5 | 70 | 0.34 | 0.76 | 18 | empty |
Compared structures
- 4C0L · Crystal structure of Drosophila Miro EF hand and cGTPase domains bound to one magnesium… · the same entry in another collection · chain A against A, TM-score 1.00
- Q8IMX7 · AlphaFold monomer V2.0 prediction for mitochondrial rho GTPase (Q8IMX7) · a predicted model of the same protein · chain A 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 Q8IMX7
- Elsewhere: RCSB PDB 4C0L · PDBe 4C0L · UniProt Q8IMX7
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