MolNFT v1 · #13150 · protein
Scallop myosin S1-ADP-P-pdm in the actin-detached conformation
1L2O · Myosin heavy chain: “Scallop myosin S1-ADP-P-pdm in the actin-detached conformation”. X-ray diffraction, 4 ligands (PDM, ADP, MG), 9 pockets (best druggability 0.84). MolNFT v1 #13150 on GenesisL1: 3D structure, binding sites and…
- PDB
- 1L2O
- 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
- PDM, ADP, MG, CA
- Pockets
- 9 · best druggability 0.84
Structure
x-ray diffraction · 3 distinct chains · 46% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Myosin heavy chain | protein | 777 | 43% helix, 12% strand | P24733 |
| B | Myosin regulatory light chain | protein | 142 | 51% helix, 1% strand | P13543 |
| C | Myosin essential light chain | protein | 153 | 58% helix, 7% strand | P07291 |
Ligands and binding sites
- PDM · 4-[4-(2,5-dioxo-pyrrolidin-1-yl)-phenylamino]-4-hydroxy-butyric acid · ligand · chains A
- ADP · Adenosine-5'-diphosphate · 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
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 874 | 0.84 | 0.86 | 118 | MG, ADP |
| 2 | 396 | 0.59 | 0.75 | 43 | empty |
| 3 | 144 | 0.52 | 0.80 | 32 | empty |
| 4 | 212 | 0.51 | 0.76 | 30 | empty |
| 5 | 110 | 0.46 | 0.78 | 19 | empty |
Interfaces
3 interfaces between chains.
- A–C · 2287 Ų buried · 28 hydrogen bonds · protein-protein
- A–B · 1779 Ų buried · 21 hydrogen bonds · protein-protein
- B–C · 229 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 1L2O · SCALLOP MYOSIN S1-ADP-p-PDM IN THE ACTIN-DETACHED CONFORMATION · the same entry in another collection · chain B against B, 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 0.98
- 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 0.89
- 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 1L2O · PDBe 1L2O · UniProt P24733 · UniProt P13543 · UniProt P07291
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