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Cryo-EM structure of phalloidin-alexa flour-546-stabilized F-actin (copolymerized)
Analyse Cryo-EM structure of phalloidin-alexa flour-546-stabilized F-actin… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6T25
- Type
- protein
- Length
- 1,845 residues
- Chains
- 10
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Actin, alpha skeletal muscle; Phalloidin
- UniProt
- P68135
- Ligands
- ADP, MG
- Pockets
- 17 · best druggability 0.82
Structure
electron microscopy · 2 distinct chains · 45% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E | Actin, alpha skeletal muscle | protein | 362 | 46% helix, 20% strand | P68135 |
| F, G, H, I, J | Phalloidin | protein | 7 | 0% helix, 0% strand | — |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 5 copies · chains A, B, C, D, E
- MG · Magnesium ion · metal · 5 copies · chains A, B, C, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 800 | 0.82 | 0.84 | 67 | empty |
| 2 | 324 | 0.79 | 0.90 | 57 | ADP, MG |
| 3 | 263 | 0.79 | 0.91 | 53 | ADP, MG |
| 4 | 391 | 0.79 | 0.88 | 43 | empty |
| 5 | 445 | 0.78 | 0.87 | 45 | empty |
Interfaces
20 interfaces between chains.
- B–D · 837 Ų buried · 12 hydrogen bonds · protein-protein
- C–E · 834 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 834 Ų buried · 12 hydrogen bonds · protein-protein
- C–D · 468 Ų buried · 6 hydrogen bonds · protein-protein
- D–E · 468 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 15 modified, 5 d-amino (D-amino acid, hydroxylation, methylation, nonstandard).
Compared structures
- 6T25 · Cryo-EM structure of phalloidin-Alexa Flour-546-stabilized F-actin (copolymerized) · the same entry in another collection · chain J against J, 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 0.96
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 6T25 · PDBe 6T25 · UniProt P68135
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