Research workbench
Cryo-EM structure of the actomyosin-V complex in the rigor state (central 3ER/2ER, young jasp-stabilized F-actin)
Analyse Cryo-EM structure of the actomyosin-V complex in the rigor state (central… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7PLZ
- Type
- protein
- Length
- 2,887 residues
- Chains
- 7
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Unconventional myosin-va; Actin, alpha skeletal muscle; Myosin light chain 6B
- UniProt
- Q02440, P68135, P14649
- Ligands
- ADP, 9UE, MG, PO4
- Pockets
- 20 · best druggability 0.79
Structure
electron microscopy · 3 distinct chains · 48% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Unconventional myosin-va | protein | 748 | 47% helix, 15% strand | Q02440 |
| C, F, G | Actin, alpha skeletal muscle | protein | 371 | 44% helix, 19% strand | P68135 |
| B, E | Myosin light chain 6B | protein | 139 | 62% helix, 7% strand | P14649 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 3 copies · chains C, F, G
- 9UE · Jasplakinolide · ligand · 3 copies · chains C, F, G
- MG · Magnesium ion · metal · 3 copies · chains C, F, G
- PO4 · Phosphate ion · ion · 3 copies · chains C, 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, 19 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 601 | 0.79 | 0.84 | 74 | empty |
| 2 | 1117 | 0.79 | 0.80 | 80 | empty |
| 3 | 1022 | 0.79 | 0.80 | 81 | empty |
| 4 | 303 | 0.78 | 0.90 | 48 | ADP, PO4, MG |
| 5 | 148 | 0.78 | 0.95 | 40 | empty |
Interfaces
8 interfaces between chains.
- A–B · 1650 Ų buried · 11 hydrogen bonds · protein-protein
- D–E · 1636 Ų buried · 13 hydrogen bonds · protein-protein
- F–G · 1213 Ų buried · 11 hydrogen bonds · protein-protein
- D–F · 934 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 930 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 modified, 1 covalent (methylation, covalent ligand).
Compared structures
- 7PLZ · Cryo-EM structure of the actomyosin-V complex in the rigor state (central 3er/2er, young… · the same entry in another collection · chain G against G, 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 0.95
- 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 Q02440
- Every structure of UniProt P68135
- Every structure of UniProt P14649
- Elsewhere: RCSB PDB 7PLZ · PDBe 7PLZ · UniProt Q02440 · UniProt P68135 · UniProt P14649
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