Research workbench
Cryo-EM structure of the actomyosin-V complex in the post-rigor transition state (appnhp, central 3ER/2ER)
Analyse Cryo-EM structure of the actomyosin-V complex in the post-rigor transition… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7PME
- Type
- protein
- Length
- 2,909 residues
- Chains
- 10
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Unconventional myosin-va; Myosin light chain 6B; Actin, alpha skeletal muscle; Phalloidin
- UniProt
- Q02440, P14649, P68135
- Ligands
- ADP, ANP, MG
- Pockets
- 20 · best druggability 0.81
Structure
electron microscopy · 4 distinct chains · 48% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Unconventional myosin-va | protein | 747 | 49% helix, 16% strand | Q02440 |
| B, E | Myosin light chain 6B | protein | 139 | 60% helix, 9% strand | P14649 |
| C, F, G | Actin, alpha skeletal muscle | protein | 372 | 43% helix, 20% strand | P68135 |
| H, I, J | Phalloidin | protein | 7 | 0% helix, 0% strand | — |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 3 copies · chains C, F, G
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 2 copies · chains A, D
- MG · Magnesium ion · metal · 7 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 | 689 | 0.81 | 0.85 | 62 | empty |
| 2 | 1106 | 0.78 | 0.80 | 79 | empty |
| 3 | 1149 | 0.78 | 0.80 | 81 | empty |
| 4 | 278 | 0.77 | 0.90 | 45 | ADP, MG |
| 5 | 360 | 0.76 | 0.86 | 58 | ADP, MG |
Interfaces
15 interfaces between chains.
- D–E · 1623 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 1614 Ų buried · 11 hydrogen bonds · protein-protein
- F–G · 1234 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 998 Ų buried · 10 hydrogen bonds · protein-protein
- D–F · 994 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 modified, 3 d-amino (D-amino acid, hydroxylation, methylation, nonstandard).
Compared structures
- 7PME · Cryo-EM structure of the actomyosin-V complex in the post-rigor transition state (AppNHp… · 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 Q02440
- Every structure of UniProt P14649
- Every structure of UniProt P68135
- Elsewhere: RCSB PDB 7PME · PDBe 7PME · UniProt Q02440 · UniProt P14649 · UniProt P68135
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