Research workbench
Cryo-EM structure of F-actin in the MG2+-ADP-BEF3- nucleotide state.
Analyse Cryo-EM structure of F-actin in the MG2+-ADP-BEF3- nucleotide state. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 8A2R
- Type
- protein
- Length
- 1,830 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Actin, alpha skeletal muscle
- UniProt
- P68135
- Ligands
- ADP, BEF, MG
- Pockets
- 20 · best druggability 0.75
Structure
electron microscopy · 1 distinct chain · 43% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C, A, B, D, E | Actin, alpha skeletal muscle | protein | 366 | 43% helix, 21% strand | P68135 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 5 copies · chains C, A, B, D, E
- BEF · Beryllium trifluoride ion · ligand · 5 copies · chains C, A, B, D, E
- MG · Magnesium 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
20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 570 | 0.75 | 0.82 | 50 | empty |
| 2 | 327 | 0.75 | 0.86 | 48 | ADP, MG, BEF |
| 3 | 313 | 0.74 | 0.87 | 49 | ADP, MG, BEF |
| 4 | 320 | 0.74 | 0.86 | 51 | ADP, MG, BEF |
| 5 | 337 | 0.74 | 0.86 | 54 | empty |
Interfaces
7 interfaces between chains.
- C–E · 1124 Ų buried · 16 hydrogen bonds · protein-protein
- C–A · 1112 Ų buried · 16 hydrogen bonds · protein-protein
- B–D · 1112 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 509 Ų buried · 10 hydrogen bonds · protein-protein
- C–D · 483 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 modified (methylation).
Compared structures
- 8A2R · Cryo-EM structure of F-actin in the Mg2+-ADP-BeF3- 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 8A2R · PDBe 8A2R · UniProt P68135
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