MolNFT v1 · #121608 · protein
Crystal structure of myosin X motor domain in pre-powerstroke state
5I0H · Unconventional myosin-X: “Crystal structure of myosin X motor domain in pre-powerstroke state”. X-ray diffraction, 4 ligands (ADP, BEF, MG), 20 pockets (best druggability 0.83). MolNFT v1 #121608 on GenesisL1: 3D structure, binding…
- PDB
- 5I0H
- Type
- protein
- Length
- 1,454 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Unconventional myosin-X
- UniProt
- Q9HD67
- Ligands
- ADP, BEF, MG, SO4
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 47% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Unconventional myosin-X | protein | 731 | 47% helix, 19% strand | Q9HD67 |
| B | Unconventional myosin-X | protein | 723 | 48% helix, 18% strand | Q9HD67 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, B
- BEF · Beryllium trifluoride ion · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 5 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 18 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1025 | 0.83 | 0.84 | 107 | EDO, SO4 |
| 2 | 638 | 0.77 | 0.83 | 61 | empty |
| 3 | 609 | 0.74 | 0.81 | 56 | empty |
| 4 | 223 | 0.64 | 0.83 | 26 | empty |
| 5 | 331 | 0.64 | 0.79 | 39 | EDO |
Interfaces
1 interface between chains.
- A–B · 1383 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 5I0H · Crystal structure of myosin X motor domain in pre-powerstroke state · the same entry in another collection · chain A against A, TM-score 1.00
- Q9HD67 · AlphaFold monomer V2.0 prediction for unconventional myosin-X (Q9HD67) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 Q9HD67
- Elsewhere: RCSB PDB 5I0H · PDBe 5I0H · UniProt Q9HD67
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