Research workbench
Cofilin decorated actin filament
Analyse Cofilin decorated actin filament in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5YU8
- Type
- protein
- Length
- 2,292 residues
- Chains
- 8
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Actin, alpha skeletal muscle; Cofilin-2
- UniProt
- P68139, P21566
- Ligands
- ADP, MG
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · 2 distinct chains · 36% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E | Actin, alpha skeletal muscle | protein | 360 | 39% helix, 19% strand | P68139 |
| H, I, J | Cofilin-2 | protein | 164 | 28% helix, 34% strand | P21566 |
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
20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1055 | 0.84 | 0.85 | 103 | MG, ADP |
| 2 | 671 | 0.82 | 0.86 | 92 | MG, ADP |
| 3 | 503 | 0.81 | 0.88 | 72 | MG, ADP |
| 4 | 297 | 0.78 | 0.90 | 53 | MG, ADP |
| 5 | 355 | 0.77 | 0.87 | 50 | empty |
Interfaces
13 interfaces between chains.
- D–I · 1123 Ų buried · 9 hydrogen bonds · protein-protein
- E–J · 1120 Ų buried · 10 hydrogen bonds · protein-protein
- C–H · 1117 Ų buried · 9 hydrogen bonds · protein-protein
- C–J · 817 Ų buried · 18 hydrogen bonds · protein-protein
- B–I · 809 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 5YU8 · Cofilin decorated actin filament · the same entry in another collection · chain E against E, TM-score 1.00
- P21566 · AlphaFold monomer V2.0 prediction for cofilin-2 (P21566) · a predicted model of the same protein · chain J against A, TM-score 0.97
- P68139 · AlphaFold monomer V2.0 prediction for actin, alpha skeletal muscle (P68139) · a predicted model of the same protein · chain B against A, TM-score 0.93
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 P68139
- Every structure of UniProt P21566
- Elsewhere: RCSB PDB 5YU8 · PDBe 5YU8 · UniProt P68139 · UniProt P21566
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