Research workbench
Bare actin filament from a partially cofilin-decorated sample
Analyse Bare actin filament from a partially cofilin-decorated sample in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6VAU
- Type
- protein
- Length
- 1,850 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Actin, alpha skeletal muscle
- UniProt
- P68135
- Ligands
- ADP, MG
- Pockets
- 13 · best druggability 0.82
Structure
electron microscopy · 1 distinct chain · 40% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, A, C, D, E | Actin, alpha skeletal muscle | protein | 370 | 40% helix, 18% strand | P68135 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 5 copies · chains B, A, C, D, E
- MG · Magnesium ion · metal · 5 copies · chains B, A, C, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 934 | 0.82 | 0.84 | 99 | empty |
| 2 | 236 | 0.77 | 0.91 | 45 | MG, ADP |
| 3 | 261 | 0.77 | 0.90 | 51 | MG, ADP |
| 4 | 250 | 0.76 | 0.90 | 51 | MG, ADP |
| 5 | 260 | 0.76 | 0.89 | 48 | MG, ADP |
Interfaces
7 interfaces between chains.
- A–C · 1231 Ų buried · 7 hydrogen bonds · protein-protein
- B–E · 1223 Ų buried · 6 hydrogen bonds · protein-protein
- B–D · 1220 Ų buried · 6 hydrogen bonds · protein-protein
- C–D · 488 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 484 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 6VAU · Bare actin filament from a partially cofilin-decorated sample · 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 E 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 6VAU · PDBe 6VAU · UniProt P68135
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