MolNFT v1 · #121609 · protein
Crystal structure of myosin X motor domain with 2IQ motifs in pre- powerstroke state
5I0I · Unconventional myosin-X: “Crystal structure of myosin X motor domain with 2IQ motifs in pre- powerstroke state”. X-ray diffraction, 4 ligands (ADP, MG, SO4), 20 pockets (best druggability 0.81). MolNFT v1 #121609 on GenesisL1: 3D…
- PDB
- 5I0I
- Type
- protein
- Length
- 1,960 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Unconventional myosin-X; Calmodulin
- UniProt
- Q9HD67, P62158
- Ligands
- ADP, MG, SO4, VO4
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 5 distinct chains · 50% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Unconventional myosin-X | protein | 784 | 49% helix, 17% strand | Q9HD67 |
| C | Calmodulin | protein | 145 | 56% helix, 7% strand | P62158 |
| E | Calmodulin | protein | 145 | 54% helix, 6% strand | P62158 |
| G | Calmodulin | protein | 43 | 23% helix, 0% strand | P62158 |
| I | Calmodulin | protein | 59 | 47% helix, 7% strand | P62158 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 8 copies · chains A, B, C, E
- VO4 · Vanadate ion · ion · 2 copies · chains A, B
- MPO · 3[N-morpholino]propane sulfonic acid · additive · 2 copies · chains A, C, 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 | 781 | 0.81 | 0.84 | 89 | empty |
| 2 | 1105 | 0.81 | 0.82 | 95 | empty |
| 3 | 492 | 0.76 | 0.83 | 53 | empty |
| 4 | 662 | 0.75 | 0.81 | 58 | SO4 |
| 5 | 805 | 0.74 | 0.79 | 67 | SO4 |
Interfaces
9 interfaces between chains.
- A–B · 1669 Ų buried · 14 hydrogen bonds · protein-protein
- A–C · 1336 Ų buried · 3 hydrogen bonds · protein-protein
- B–E · 1240 Ų buried · 3 hydrogen bonds · protein-protein
- A–G · 553 Ų buried · 4 hydrogen bonds · protein-protein
- B–I · 462 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 5I0I · Crystal structure of myosin X motor domain with 2IQ motifs in pre-powerstroke state · the same entry in another collection · chain C against C, TM-score 1.00
- Q9HD67 · AlphaFold monomer V2.0 prediction for unconventional myosin-X (Q9HD67) · a predicted model of the same protein · chain A 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
- Every structure of UniProt P62158
- Elsewhere: RCSB PDB 5I0I · PDBe 5I0I · UniProt Q9HD67 · UniProt P62158
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