Research workbench
Cryo-EM structure of the actomyosin-V complex in the strong-ADP state (central 1ER, class 3)
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
- 7PM8
- Type
- protein
- Length
- 1,261 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phalloidin; Unconventional myosin-va; Myosin light chain 6B; Actin, alpha skeletal muscle
- UniProt
- Q02440, P14649, P68135
- Ligands
- ADP, MG
- Pockets
- 14 · best druggability 0.78
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 | — |
| A | Unconventional myosin-va | protein | 743 | 48% helix, 16% strand | Q02440 |
| B | Myosin light chain 6B | protein | 139 | 60% helix, 8% strand | P14649 |
| C | Actin, alpha skeletal muscle | protein | 372 | 45% 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
14 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1194 | 0.78 | 0.80 | 83 | empty |
| 2 | 350 | 0.75 | 0.86 | 52 | ADP, MG |
| 3 | 686 | 0.72 | 0.78 | 63 | empty |
| 4 | 376 | 0.67 | 0.81 | 50 | MG, ADP |
| 5 | 60 | 0.65 | 0.94 | 21 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1565 Ų buried · 13 hydrogen bonds · protein-protein
- A–C · 1074 Ų buried · 13 hydrogen bonds · protein-protein
- H–C · 245 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 3 modified, 1 d-amino (D-amino acid, hydroxylation, methylation, nonstandard).
Compared structures
- 7PM8 · 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
- 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 0.95
- Q02440 · AlphaFold monomer V2.0 prediction for unconventional myosin-va (Q02440) · a predicted model of the same protein · chain A against A, TM-score 0.93
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 Q02440
- Every structure of UniProt P14649
- Every structure of UniProt P68135
- Elsewhere: RCSB PDB 7PM8 · PDBe 7PM8 · UniProt Q02440 · UniProt P14649 · UniProt P68135
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