Research workbench
Cryo-EM structure of the actomyosin-V complex in the strong-ADP state (central 3ER/2ER)
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
- 7PM6
- Type
- protein
- Length
- 2,907 residues
- Chains
- 10
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Myosin light chain 6B; Unconventional myosin-va; Actin, alpha skeletal muscle; Phalloidin
- UniProt
- P14649, Q02440, P68135
- Ligands
- ADP, MG
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · 4 distinct chains · 47% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, E | Myosin light chain 6B | protein | 139 | 60% helix, 9% strand | P14649 |
| A, D | Unconventional myosin-va | protein | 746 | 48% helix, 16% strand | Q02440 |
| C, F, G | Actin, alpha skeletal muscle | protein | 372 | 41% helix, 20% strand | P68135 |
| H, I, J | Phalloidin | protein | 7 | 0% helix, 0% strand | — |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 5 copies · chains A, C, D, F, G
- MG · Magnesium ion · metal · 5 copies · chains A, C, D, F, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1170 | 0.85 | 0.85 | 104 | empty |
| 2 | 1082 | 0.79 | 0.81 | 72 | empty |
| 3 | 1178 | 0.78 | 0.80 | 84 | empty |
| 4 | 264 | 0.74 | 0.88 | 47 | ADP, MG |
| 5 | 362 | 0.73 | 0.85 | 52 | ADP, MG |
Interfaces
15 interfaces between chains.
- B–A · 1779 Ų buried · 22 hydrogen bonds · protein-protein
- E–D · 1769 Ų buried · 19 hydrogen bonds · protein-protein
- F–G · 1206 Ų buried · 10 hydrogen bonds · protein-protein
- D–F · 1042 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 1042 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 modified, 3 d-amino (D-amino acid, hydroxylation, methylation, nonstandard).
Compared structures
- 7PM6 · Cryo-EM structure of the actomyosin-V complex in the strong-ADP state (central 3er/2er) · the same entry in another collection · chain J against J, TM-score 1.00
- P68135 · AlphaFold monomer V2.0 prediction for actin, alpha skeletal muscle (P68135) · a predicted model of the same protein · chain G against A, TM-score 0.96
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 7PM6 · PDBe 7PM6 · UniProt P14649 · UniProt Q02440 · UniProt P68135
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