MolNFT v1 · #164567 · protein
Cryo-EM structure of phalloidin-stabilized F-actin (copolymerized)
6T1Y · Actin, alpha skeletal muscle: “Cryo-EM structure of phalloidin-stabilized F-actin (copolymerized)”. Electron microscopy, 2 ligands (ADP, MG), 17 pockets (best druggability 0.79). MolNFT v1 #164567 on GenesisL1: 3D structure, binding…
- PDB
- 6T1Y
- Type
- protein
- Length
- 1,890 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 0.79
Structure
electron microscopy · 2 distinct chains · 41% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E | Actin, alpha skeletal muscle | protein | 371 | 42% 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, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 332 | 0.79 | 0.90 | 46 | empty |
| 2 | 306 | 0.78 | 0.89 | 47 | empty |
| 3 | 330 | 0.78 | 0.89 | 52 | ADP, MG |
| 4 | 420 | 0.78 | 0.86 | 45 | empty |
| 5 | 286 | 0.78 | 0.90 | 52 | empty |
Interfaces
20 interfaces between chains.
- B–D · 1122 Ų buried · 15 hydrogen bonds · protein-protein
- C–E · 1119 Ų buried · 15 hydrogen bonds · protein-protein
- A–C · 1118 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 472 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 471 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 15 modified, 5 d-amino (D-amino acid, hydroxylation, methylation, nonstandard).
Compared structures
- 6T1Y · Cryo-EM structure of phalloidin-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 B against A, TM-score 0.95
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 6T1Y · PDBe 6T1Y · UniProt P68135
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