MolNFT v1 · #85762 · protein
ADP-bound C-terminal domain of actin-related protein ARP8 from S. cerevisiae
4AM7 · Actin-like protein ARP8: “ADP-bound C-terminal domain of actin-related protein ARP8 from S. cerevisiae”. X-ray diffraction, 1 ligand (ADP), 20 pockets (best druggability 0.85). MolNFT v1 #85762 on GenesisL1: 3D structure, binding…
- PDB
- 4AM7
- Type
- protein
- Length
- 1,246 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Actin-like protein ARP8
- UniProt
- Q12386
- Ligands
- ADP
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 1 distinct chain · 41% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Actin-like protein ARP8 | protein | 623 | 41% helix, 15% strand | Q12386 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1138 | 0.85 | 0.86 | 92 | ADP |
| 2 | 1123 | 0.85 | 0.86 | 95 | ADP |
| 3 | 634 | 0.81 | 0.86 | 56 | empty |
| 4 | 530 | 0.79 | 0.86 | 43 | empty |
| 5 | 132 | 0.51 | 0.80 | 25 | empty |
Interfaces
1 interface between chains.
- A–B · 640 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 4AM7 · ADP-bound C-terminal domain of actin-related protein ARP8 from S. cerevisiae · the same entry in another collection · chain A against A, TM-score 1.00
- Q12386 · AlphaFold monomer V2.0 prediction for actin-like protein ARP8 (Q12386) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 Q12386
- Elsewhere: RCSB PDB 4AM7 · PDBe 4AM7 · UniProt Q12386
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