Research workbench
Cryo-EM structure of cardiac muscle alpha-actin
Analyse Cryo-EM structure of cardiac muscle alpha-actin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 8DMY
- Type
- protein
- Length
- 1,494 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.07
- Source
- Bos taurus
- Molecule
- Actin, alpha cardiac muscle 1
- EC
- 3.6.4.-
- UniProt
- Q3ZC07
- Ligands
- ADP, MG
- Pockets
- 11 · best druggability 0.79
Structure
electron microscopy · resolution 3.07 · 2 distinct chains · 41% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Actin, alpha cardiac muscle 1 (EC 3.6.4.-) | protein | 374 | 41% helix, 20% strand | Q3ZC07 |
| C, D | Actin, alpha cardiac muscle 1 (EC 3.6.4.-) | protein | 373 | 41% helix, 20% strand | Q3ZC07 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 4 copies · chains A, 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, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 420 | 0.79 | 0.88 | 54 | ADP, MG |
| 2 | 447 | 0.78 | 0.87 | 61 | ADP, MG |
| 3 | 365 | 0.77 | 0.88 | 52 | ADP, MG |
| 4 | 403 | 0.77 | 0.87 | 54 | ADP, MG |
| 5 | 395 | 0.73 | 0.83 | 38 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1227 Ų buried · 6 hydrogen bonds · protein-protein
- C–D · 1223 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 379 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 368 Ų buried · 2 hydrogen bonds · protein-protein
- A–D · 353 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (methylation).
Compared structures
- Q3ZC07 · AlphaFold monomer V2.0 prediction for actin, alpha cardiac muscle 1 (Q3ZC07) · a predicted model of the same protein · chain C 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 Q3ZC07
- Elsewhere: RCSB PDB 8DMY · PDBe 8DMY · UniProt Q3ZC07
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