MolNFT v1 · #185242 · protein
Cryo-EM structure of the actomyosin-V complex in the rigor state (central 1ER, young jasp-stabilized F-actin, class 1)
7PM0 · Myosin light chain 6B: “Cryo-EM structure of the actomyosin-V complex in the rigor state (central 1ER, young jasp-stabilized F-actin…”. Electron microscopy, 4 ligands (ADP, 9UE, MG), 13 pockets (best druggability 0.78). MolNFT v1…
- PDB
- 7PM0
- Type
- protein
- Length
- 1,261 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Myosin light chain 6B; Unconventional myosin-va; Actin, alpha skeletal muscle
- UniProt
- P14649, Q02440, P68135
- Ligands
- ADP, 9UE, MG, PO4
- Pockets
- 13 · best druggability 0.78
Structure
electron microscopy · 3 distinct chains · 49% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Myosin light chain 6B | protein | 139 | 60% helix, 7% strand | P14649 |
| A | Unconventional myosin-va | protein | 751 | 48% helix, 15% strand | Q02440 |
| C | Actin, alpha skeletal muscle | protein | 371 | 44% helix, 20% strand | P68135 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · chains C
- 9UE · Jasplakinolide · ligand · chains C
- MG · Magnesium ion · metal · chains C
- PO4 · Phosphate ion · ion · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1113 | 0.78 | 0.80 | 75 | empty |
| 2 | 413 | 0.76 | 0.86 | 57 | ADP, PO4, MG |
| 3 | 651 | 0.72 | 0.79 | 56 | empty |
| 4 | 64 | 0.70 | 0.97 | 22 | empty |
| 5 | 333 | 0.61 | 0.78 | 44 | empty |
Interfaces
2 interfaces between chains.
- B–A · 1679 Ų buried · 15 hydrogen bonds · protein-protein
- A–C · 1020 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (methylation).
Compared structures
- 7PM0 · Cryo-EM structure of the actomyosin-V complex in the rigor state (central 1er, young… · the same entry in another collection · chain B against B, 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 0.94
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 7PM0 · PDBe 7PM0 · UniProt P14649 · UniProt Q02440 · UniProt P68135
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