Research workbench
Cryo-EM structure of young jasp-stabilized F-actin (central 3ER)
Analyse Cryo-EM structure of young jasp-stabilized F-actin (central 3ER) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7PM3
- Type
- protein
- Length
- 1,113 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Actin, alpha skeletal muscle
- UniProt
- P68135
- Ligands
- ADP, 9UE, MG, PO4
- Pockets
- 11 · best druggability 0.81
Structure
electron microscopy · 1 distinct chain · 43% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, C, D | Actin, alpha skeletal muscle | protein | 371 | 43% helix, 19% strand | P68135 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 3 copies · chains B, C, D
- 9UE · Jasplakinolide · ligand · 3 copies · chains B, C, D
- MG · Magnesium ion · metal · 3 copies · chains B, C, D
- PO4 · Phosphate ion · ion · 3 copies · chains B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 777 | 0.81 | 0.84 | 78 | empty |
| 2 | 343 | 0.77 | 0.88 | 50 | ADP, PO4, MG |
| 3 | 319 | 0.75 | 0.87 | 50 | ADP, PO4, MG |
| 4 | 312 | 0.74 | 0.87 | 48 | ADP, PO4, MG |
| 5 | 433 | 0.73 | 0.83 | 42 | empty |
Interfaces
3 interfaces between chains.
- B–D · 1016 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 484 Ų buried · 5 hydrogen bonds · protein-protein
- C–D · 478 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 modified (methylation).
Compared structures
- 7PM3 · Cryo-EM structure of young JASP-stabilized F-actin (central 3er) · 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 0.95
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 P68135
- Elsewhere: RCSB PDB 7PM3 · PDBe 7PM3 · UniProt P68135
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