MolNFT v1 · #172778 · protein
Structure of the lifeact-F-actin complex
7AD9: “Structure of the lifeact-F-actin complex”. Electron microscopy, 3 ligands (ADP, MG, PO4), 20 pockets (best druggability 0.84). MolNFT v1 #172778 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7AD9
- Type
- protein
- Length
- 1,970 residues
- Chains
- 15
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lifeact; Actin, alpha skeletal muscle; Phalloidin
- UniProt
- P68135
- Ligands
- ADP, MG, PO4
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · 3 distinct chains · 44% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, L, E, G | Lifeact | protein | 16 | 81% helix, 0% strand | — |
| B, D, H, F, I | Actin, alpha skeletal muscle | protein | 371 | 43% helix, 19% strand | P68135 |
| O, P, Q, R, S | Phalloidin | protein | 7 | 0% helix, 0% strand | — |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 5 copies · chains B, D, H, F, I
- MG · Magnesium ion · metal · 5 copies · chains B, D, H, F, I
- PO4 · Phosphate ion · ion · 5 copies · chains B, D, H, F, I
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 614 | 0.84 | 0.88 | 69 | empty |
| 2 | 1163 | 0.83 | 0.84 | 95 | empty |
| 3 | 578 | 0.83 | 0.88 | 65 | empty |
| 4 | 360 | 0.79 | 0.89 | 52 | ADP, MG, PO4 |
| 5 | 371 | 0.79 | 0.88 | 53 | ADP, MG, PO4 |
Interfaces
28 interfaces between chains.
- H–I · 1287 Ų buried · 16 hydrogen bonds · protein-protein
- B–H · 1284 Ų buried · 18 hydrogen bonds · protein-protein
- D–F · 1269 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 498 Ų buried · 4 hydrogen bonds · protein-protein
- G–I · 494 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
- 7AD9 · Structure of the Lifeact-F-actin complex · the same entry in another collection · chain S against S, TM-score 1.00
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 7AD9 · PDBe 7AD9 · UniProt P68135
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