Research workbench
Scallop myosin S1 complexed with MGADP:VANADATE-transition state
Analyse Scallop myosin S1 complexed with MGADP:VANADATE-transition state in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1DFL
- Type
- protein
- Length
- 2,112 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Myosin head
- UniProt
- P24733, P13543, P07291
- Ligands
- ADP, MG, CA, VO4
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 4 distinct chains · 49% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Myosin head | protein | 772 | 48% helix, 13% strand | P24733 |
| Y, W | Myosin head | protein | 136 | 54% helix, 4% strand | P13543 |
| Z, X | Myosin head | protein | 151 | 54% helix, 4% strand | P07291 |
| B | Myosin head | protein | 766 | 48% helix, 13% strand | P24733 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 4 copies · chains A, Y, B, W
- CA · Calcium ion · metal · 2 copies · chains Z, X
- VO4 · Vanadate ion · ion · 2 copies · chains A, 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, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 968 | 0.83 | 0.84 | 142 | empty |
| 2 | 894 | 0.81 | 0.84 | 120 | empty |
| 3 | 785 | 0.80 | 0.84 | 116 | empty |
| 4 | 592 | 0.79 | 0.85 | 96 | empty |
| 5 | 493 | 0.78 | 0.86 | 84 | empty |
Interfaces
7 interfaces between chains.
- B–X · 522 Ų buried · 0 hydrogen bonds · protein-protein
- A–Z · 515 Ų buried · 0 hydrogen bonds · protein-protein
- A–Y · 240 Ų buried · 1 hydrogen bond · protein-protein
- B–W · 231 Ų buried · 1 hydrogen bond · protein-protein
- W–X · 101 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 1DFL · Scallop myosin S1 complexed with MGADP:VANADATE-transition state · the same entry in another collection · chain X against X, 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 0.98
- 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 0.94
- 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 0.89
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 1DFL · PDBe 1DFL · UniProt P24733 · UniProt P13543 · UniProt P07291
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