Research workbench
Cryo-EM structure of F-actin in the Ca2+-ADP nucleotide state.
Analyse Cryo-EM structure of F-actin in the Ca2+-ADP nucleotide state. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 8A2Z
- Type
- protein
- Length
- 1,830 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.15
- Source
- Oryctolagus cuniculus
- Molecule
- Actin, alpha skeletal muscle
- UniProt
- P68135
- Ligands
- ADP, CA
- Pockets
- 19 · best druggability 0.80
Structure
electron microscopy · resolution 2.15 · 1 distinct chain · 44% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C, A, B, D, E | Actin, alpha skeletal muscle | protein | 366 | 44% helix, 20% strand | P68135 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 5 copies · chains C, A, B, D, E
- CA · Calcium ion · metal · 5 copies · chains C, A, B, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 584 | 0.80 | 0.86 | 87 | empty |
| 2 | 237 | 0.75 | 0.89 | 44 | ADP, CA |
| 3 | 229 | 0.75 | 0.89 | 46 | ADP, CA |
| 4 | 225 | 0.73 | 0.88 | 39 | ADP, CA |
| 5 | 311 | 0.73 | 0.86 | 47 | empty |
Interfaces
7 interfaces between chains.
- C–E · 1116 Ų buried · 16 hydrogen bonds · protein-protein
- B–D · 1107 Ų buried · 15 hydrogen bonds · protein-protein
- C–A · 1101 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 481 Ų buried · 8 hydrogen bonds · protein-protein
- C–B · 472 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 modified (methylation).
Compared structures
- 8A2Z · Cryo-EM structure of F-actin in the CA2+-ADP nucleotide state. · the same entry in another collection · chain E against E, TM-score 1.00
- P68135 · AlphaFold monomer V2.0 prediction for actin, alpha skeletal muscle (P68135) · a predicted model of the same protein · chain A against A, TM-score 0.96
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 8A2Z · PDBe 8A2Z · UniProt P68135
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.