Research workbench
Scallop myosin S1-amppnp in the actin-detached conformation
Analyse Scallop myosin S1-amppnp in the actin-detached conformation in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1KQM
- Type
- protein
- Length
- 1,072 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Myosin heavy chain; Myosin regulatory light chain; Myosin essential light chain
- UniProt
- P24733, P13543, P07291
- Ligands
- ANP, MG, CA
- Pockets
- 18 · best druggability 0.86
Structure
x-ray diffraction · 3 distinct chains · 42% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Myosin heavy chain | protein | 777 | 42% helix, 12% strand | P24733 |
| B | Myosin regulatory light chain | protein | 142 | 44% helix, 3% strand | P13543 |
| C | Myosin essential light chain | protein | 153 | 44% helix, 5% strand | P07291 |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · chains A
- MG · Magnesium ion · metal · 2 copies · chains A, B
- CA · Calcium ion · metal · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 999 | 0.86 | 0.87 | 128 | MG, ANP |
| 2 | 289 | 0.77 | 0.89 | 32 | empty |
| 3 | 154 | 0.74 | 0.91 | 40 | empty |
| 4 | 747 | 0.70 | 0.77 | 69 | empty |
| 5 | 572 | 0.67 | 0.77 | 56 | empty |
Interfaces
3 interfaces between chains.
- A–C · 2238 Ų buried · 29 hydrogen bonds · protein-protein
- A–B · 1620 Ų buried · 16 hydrogen bonds · protein-protein
- B–C · 255 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 1KQM · Scallop myosin S1-amppnp in the actin-detached conformation · 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 C 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 B against A, TM-score 0.87
- 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 0.81
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 1KQM · PDBe 1KQM · UniProt P24733 · UniProt P13543 · UniProt P07291
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