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Structural basis for GTP hydrolysis and conformational change of mitofusin 1 in mediating mitochondrial fusion
Analyse Structural basis for GTP hydrolysis and conformational change of mitofusin 1 in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5YEW
- Type
- protein
- Length
- 1,166 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mitofusin-1,MITOFUSIN-1 fusion protein
- EC
- 3.6.5.-
- UniProt
- Q8IWA4
- Ligands
- GDP, BEF, K, MG
- Pockets
- 15 · best druggability 0.78
Structure
x-ray diffraction · 3 distinct chains · 58% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Mitofusin-1,MITOFUSIN-1 fusion protein (EC 3.6.5.-) | protein | 390 | 58% helix, 13% strand | Q8IWA4 |
| B | Mitofusin-1,MITOFUSIN-1 fusion protein (EC 3.6.5.-) | protein | 387 | 59% helix, 13% strand | Q8IWA4 |
| C | Mitofusin-1,MITOFUSIN-1 fusion protein (EC 3.6.5.-) | protein | 389 | 58% helix, 13% strand | Q8IWA4 |
Ligands and binding sites
- GDP · Guanosine-5'-diphosphate · ligand · 3 copies · chains A, B, C
- BEF · Beryllium trifluoride ion · ligand · 3 copies · chains A, B, C
- K · Potassium ion · metal · 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
15 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 909 | 0.78 | 0.81 | 93 | GDP, BEF, K, MG |
| 2 | 564 | 0.66 | 0.76 | 62 | empty |
| 3 | 127 | 0.55 | 0.83 | 26 | GDP, BEF, K, MG |
| 4 | 87 | 0.53 | 0.84 | 17 | empty |
| 5 | 98 | 0.50 | 0.82 | 20 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1580 Ų buried · 27 hydrogen bonds · protein-protein
- B–C · 322 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 285 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 5YEW · Structural basis for GTP hydrolysis and conformational change of mitofusin 1 in mediating… · the same entry in another collection · chain A against A, TM-score 1.00
- Q8IWA4 · AlphaFold monomer V2.0 prediction for mitofusin-1 (Q8IWA4) · a predicted model of the same protein · chain B against A, TM-score 0.64
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 Q8IWA4
- Elsewhere: RCSB PDB 5YEW · PDBe 5YEW · UniProt Q8IWA4
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