Research workbench
Cardiac muscle myosin S1 fragment in the pre-powerstroke state co- crystallized with the activator omecamtiv mecarbil
Analyse Cardiac muscle myosin S1 fragment in the pre-powerstroke state co- crystallized… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5N69
- Type
- protein
- Length
- 1,842 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Myosin-7; Myosin light chain 3
- UniProt
- Q9BE39, P85100
- Ligands
- ADP, 2OW, TCE, MG, VO4
- Pockets
- 20 · best druggability 0.88
Structure
x-ray diffraction · 4 distinct chains · 51% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Myosin-7 | protein | 760 | 50% helix, 15% strand | Q9BE39 |
| B | Myosin-7 | protein | 765 | 50% helix, 15% strand | Q9BE39 |
| G | Myosin light chain 3 | protein | 156 | 56% helix, 6% strand | P85100 |
| H | Myosin light chain 3 | protein | 161 | 54% helix, 5% strand | P85100 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, B
- 2OW · Methyl 4-(2-fluoro-3-{[(6-methylpyridin-3-yl) carbamoyl]amino}benzyl)piperazine-1-carboxylate · ligand · 2 copies · chains A, B
- TCE · 3,3',3''-phosphanetriyltripropanoic acid · ligand · chains B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- VO4 · Vanadate ion · ion · 2 copies · chains A, B
- GOL · Glycerol · additive · 25 copies · chains A, B, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 915 | 0.88 | 0.90 | 131 | 2OW, GOL |
| 2 | 183 | 0.76 | 0.92 | 32 | 2OW |
| 3 | 459 | 0.74 | 0.83 | 61 | GOL |
| 4 | 502 | 0.74 | 0.82 | 68 | GOL |
| 5 | 251 | 0.73 | 0.88 | 26 | empty |
Interfaces
4 interfaces between chains.
- A–H · 1885 Ų buried · 28 hydrogen bonds · protein-protein
- B–G · 1836 Ų buried · 25 hydrogen bonds · protein-protein
- A–B · 1491 Ų buried · 8 hydrogen bonds · protein-protein
- B–H · 29 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (methylation).
Compared structures
- 5N69 · Cardiac muscle myosin S1 fragment in the pre-powerstroke state co-crystallized with the… · the same entry in another collection · chain H against H, TM-score 1.00
- P85100 · AlphaFold monomer V2.0 prediction for myosin light chain 3 (P85100) · a predicted model of the same protein · chain G against A, TM-score 0.98
- Q9BE39 · AlphaFold monomer V2.0 prediction for myosin-7 (Q9BE39) · a predicted model of the same protein · chain B against A, TM-score 0.96
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 Q9BE39
- Every structure of UniProt P85100
- Elsewhere: RCSB PDB 5N69 · PDBe 5N69 · UniProt Q9BE39 · UniProt P85100
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