MolNFT v1 · #171087 · protein
Skeletal myosin bound to mph-220, mgadp-VO4
6YSY · Myosin-4: “Skeletal myosin bound to mph-220, mgadp-VO4”. X-ray diffraction, 4 ligands (ADP, PJT, MG), 6 pockets (best druggability 0.81). MolNFT v1 #171087 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6YSY
- Type
- protein
- Length
- 922 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Myosin-4; Myosin light chain 1/3, skeletal muscle isoform
- UniProt
- Q28641, P02602
- Ligands
- ADP, PJT, MG, VO4
- Pockets
- 6 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 49% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Myosin-4 | protein | 767 | 49% helix, 15% strand | Q28641 |
| B | Myosin light chain 1/3, skeletal muscle isoform | protein | 155 | 54% helix, 6% strand | P02602 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · chains A
- PJT · (9~{S})-5-methyl-12-(4-morpholin-4-ylphenyl)-9-oxidanyl-4-thia-2,12-diazatricyclo[7.3.0.0^{3, 7}]dodeca-1,3(7),5-trien-8-one · ligand · chains A
- MG · Magnesium ion · metal · chains A
- VO4 · Vanadate ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 996 | 0.81 | 0.82 | 100 | empty |
| 2 | 642 | 0.78 | 0.83 | 77 | PJT |
| 3 | 396 | 0.68 | 0.81 | 51 | ADP, VO4, MG |
| 4 | 116 | 0.50 | 0.81 | 26 | empty |
| 5 | 99 | 0.38 | 0.76 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 1566 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (methylation).
Compared structures
- 6YSY · Skeletal Myosin bound to MPH-220, MgADP-VO4 · the same entry in another collection · chain A against A, TM-score 1.00
- P02602 · AlphaFold monomer V2.0 prediction for myosin light chain 1/3, skeletal muscle isoform… · a predicted model of the same protein · chain B against A, TM-score 0.98
- Q28641 · AlphaFold monomer V2.0 prediction for myosin-4 (Q28641) · a predicted model of the same protein · chain A against A, TM-score 0.95
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 Q28641
- Every structure of UniProt P02602
- Elsewhere: RCSB PDB 6YSY · PDBe 6YSY · UniProt Q28641 · UniProt P02602
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