Research workbench
Nucleotide-free scallop myosin S1-near rigor state
Analyse Nucleotide-free scallop myosin S1-near rigor state in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1DFK
- Type
- protein
- Length
- 1,019 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Myosin head
- UniProt
- P24733, P13543, P07291
- Ligands
- CA
- Pockets
- 10 · best druggability 0.79
Structure
x-ray diffraction · 3 distinct chains · 51% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Myosin head | protein | 728 | 49% helix, 14% strand | P24733 |
| Y | Myosin head | protein | 139 | 53% helix, 4% strand | P13543 |
| Z | Myosin head | protein | 152 | 53% helix, 4% strand | P07291 |
Ligands and binding sites
- CA · Calcium ion · metal · chains Z
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 962 | 0.79 | 0.81 | 125 | empty |
| 2 | 532 | 0.75 | 0.83 | 74 | empty |
| 3 | 410 | 0.75 | 0.85 | 61 | empty |
| 4 | 1144 | 0.73 | 0.77 | 123 | empty |
| 5 | 476 | 0.72 | 0.82 | 58 | empty |
Interfaces
3 interfaces between chains.
- A–Z · 589 Ų buried · 0 hydrogen bonds · protein-protein
- A–Y · 236 Ų buried · 1 hydrogen bond · protein-protein
- Y–Z · 98 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 1DFK · Nucleotide-free scallop myosin S1-near rigor state · the same entry in another collection · chain A against A, TM-score 1.00
- P07291 · AlphaFold monomer V2.0 prediction for myosin essential light chain, striated adductor… · a predicted model of the same protein · chain Z against A, TM-score 0.97
- P13543 · AlphaFold monomer V2.0 prediction for myosin regulatory light chain, striated adductor… · a predicted model of the same protein · chain Y against A, TM-score 0.88
- P24733 · AlphaFold monomer V2.0 prediction for myosin heavy chain, striated muscle (P24733) · a predicted model of the same protein · chain A against A, TM-score 0.80
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 P24733
- Every structure of UniProt P13543
- Every structure of UniProt P07291
- Elsewhere: RCSB PDB 1DFK · PDBe 1DFK · UniProt P24733 · UniProt P13543 · UniProt P07291
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