Research workbench
Cryo-EM structure of the actomyosin-V complex in the strong-ADP state (central 1ER, class 2)
Analyse Cryo-EM structure of the actomyosin-V complex in the strong-ADP state (central… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7PM7
- Type
- protein
- Length
- 1,261 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phalloidin; Myosin light chain 6B; Unconventional myosin-va; Actin, alpha skeletal muscle
- UniProt
- P14649, Q02440, P68135
- Ligands
- ADP, MG
- Pockets
- 15 · best druggability 0.79
Structure
electron microscopy · 4 distinct chains · 48% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | Phalloidin | protein | 7 | 0% helix, 0% strand | — |
| B | Myosin light chain 6B | protein | 139 | 60% helix, 8% strand | P14649 |
| A | Unconventional myosin-va | protein | 743 | 48% helix, 15% strand | Q02440 |
| C | Actin, alpha skeletal muscle | protein | 372 | 44% helix, 20% strand | P68135 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, C
- MG · Magnesium ion · metal · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1099 | 0.79 | 0.81 | 78 | empty |
| 2 | 393 | 0.74 | 0.85 | 57 | ADP, MG |
| 3 | 595 | 0.71 | 0.79 | 62 | empty |
| 4 | 280 | 0.61 | 0.79 | 39 | empty |
| 5 | 271 | 0.55 | 0.76 | 30 | empty |
Interfaces
3 interfaces between chains.
- B–A · 1643 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 1045 Ų buried · 12 hydrogen bonds · protein-protein
- H–C · 242 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 modified, 1 d-amino (D-amino acid, hydroxylation, methylation, nonstandard).
Compared structures
- 7PM7 · Cryo-EM structure of the actomyosin-V complex in the strong-ADP state (central 1er, class… · the same entry in another collection · chain H against H, TM-score 1.00
- P68135 · AlphaFold monomer V2.0 prediction for actin, alpha skeletal muscle (P68135) · a predicted model of the same protein · chain C against A, TM-score 0.96
- Q02440 · AlphaFold monomer V2.0 prediction for unconventional myosin-va (Q02440) · a predicted model of the same protein · chain A against A, TM-score 0.94
- P14649 · AlphaFold monomer V2.0 prediction for myosin light chain 6B (P14649) · a predicted model of the same protein · chain B against A, TM-score 0.94
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 P14649
- Every structure of UniProt Q02440
- Every structure of UniProt P68135
- Elsewhere: RCSB PDB 7PM7 · PDBe 7PM7 · UniProt P14649 · UniProt Q02440 · UniProt P68135
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.