Research workbench
Cryo-EM structures of the ACTIN:TROPOMYOSIN filament reveal the mechanism for the transition from C- to M-state
Analyse Cryo-EM structures of the ACTIN:TROPOMYOSIN filament reveal the mechanism for… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3J4K
- Type
- protein
- Length
- 2,147 residues
- Chains
- 7
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Actin, alpha skeletal muscle; Tropomyosin
- UniProt
- P68135
- Ligands
- ADP
- Pockets
- 20 · best druggability 0.80
Structure
electron microscopy · 2 distinct chains · 53% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E | Actin, alpha skeletal muscle | protein | 375 | 36% helix, 17% strand | P68135 |
| F, G | Tropomyosin | protein | 136 | 99% helix, 0% strand | — |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 5 copies · chains A, B, C, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 921 | 0.80 | 0.82 | 96 | empty |
| 2 | 705 | 0.79 | 0.83 | 74 | empty |
| 3 | 549 | 0.77 | 0.83 | 53 | empty |
| 4 | 167 | 0.75 | 0.93 | 40 | ADP |
| 5 | 159 | 0.75 | 0.93 | 40 | ADP |
Interfaces
9 interfaces between chains.
- F–G · 1362 Ų buried · 1 hydrogen bond · protein-protein
- D–E · 1079 Ų buried · 46 hydrogen bonds · protein-protein
- C–D · 1033 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 927 Ų buried · 13 hydrogen bonds · protein-protein
- A–D · 473 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 3J4K · Cryo-EM structures of the actin:tropomyosin filament reveal the mechanism for the… · 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 D 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 P68135
- Elsewhere: RCSB PDB 3J4K · PDBe 3J4K · UniProt P68135
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