MolNFT v2 · #226654 · protein
INF2 at the Barbed End of F-Actin
9AZ4 · Actin, alpha skeletal muscle: “INF2 at the Barbed End of F-Actin”. Electron microscopy at 3.37, 2 ligands (ADP, MG), 20 pockets (best druggability 0.79). MolNFT v2 #226654 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 9AZ4
- Type
- protein
- Length
- 3,015 residues
- Chains
- 8
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.37
- Source
- Homo sapiens; Oryctolagus cuniculus
- Molecule
- Actin, alpha skeletal muscle; Inverted formin-2
- EC
- 3.6.4.-
- UniProt
- P68135, Q27J81
- Ligands
- ADP, MG
- Pockets
- 20 · best druggability 0.79
Structure
electron microscopy · resolution 3.37 · 3 distinct chains · 58% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Actin, alpha skeletal muscle (EC 3.6.4.-) | protein | 371 | 40% helix, 20% strand | P68135 |
| G | Inverted formin-2 | protein | 393 | 67% helix, 2% strand | Q27J81 |
| H | Inverted formin-2 | protein | 396 | 65% helix, 2% strand | Q27J81 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 6 copies · chains A, B, C, D, E, F
- MG · Magnesium ion · metal · 6 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 520 | 0.79 | 0.86 | 72 | empty |
| 2 | 289 | 0.77 | 0.89 | 51 | ADP, MG |
| 3 | 256 | 0.76 | 0.90 | 46 | ADP, MG |
| 4 | 87 | 0.76 | 0.97 | 20 | empty |
| 5 | 272 | 0.76 | 0.89 | 48 | ADP, MG |
Interfaces
17 interfaces between chains.
- G–H · 4632 Ų buried · 47 hydrogen bonds · protein-protein
- F–H · 1312 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 1220 Ų buried · 7 hydrogen bonds · protein-protein
- B–D · 1217 Ų buried · 12 hydrogen bonds · protein-protein
- D–F · 1199 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 modified, 4 covalent (methylation, covalent ligand).
Compared structures
- P68135 · AlphaFold monomer V2.0 prediction for actin, alpha skeletal muscle (P68135) · a predicted model of the same protein · chain F against A, TM-score 0.97
- Q27J81 · AlphaFold monomer V2.0 prediction for inverted formin-2 (Q27J81) · a predicted model of the same protein · chain H against A, TM-score 0.75
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
- Every structure of UniProt Q27J81
- Elsewhere: RCSB PDB 9AZ4 · PDBe 9AZ4 · UniProt P68135 · UniProt Q27J81
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