MolNFT v1 · #76118 · protein
Crystal structure of actin-related protein ARP4 from S. cerevisiae complexed with ATP
3QB0 · Actin-related protein 4: “Crystal structure of actin-related protein ARP4 from S. cerevisiae complexed with ATP”. X-ray diffraction, 2 ligands (ATP, CA), 20 pockets (best druggability 0.86). MolNFT v1 #76118 on GenesisL1: 3D…
- PDB
- 3QB0
- Type
- protein
- Length
- 1,717 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Actin-related protein 4
- UniProt
- P80428
- Ligands
- ATP, CA
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 4 distinct chains · 36% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Actin-related protein 4 | protein | 427 | 37% helix, 19% strand | P80428 |
| B | Actin-related protein 4 | protein | 430 | 35% helix, 19% strand | P80428 |
| C | Actin-related protein 4 | protein | 430 | 36% helix, 19% strand | P80428 |
| D | Actin-related protein 4 | protein | 430 | 36% helix, 19% strand | P80428 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 4 copies · chains A, B, C, D
- CA · Calcium ion · metal · 4 copies · chains A, D, C, 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, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 951 | 0.86 | 0.87 | 108 | ATP, CA |
| 2 | 1037 | 0.84 | 0.85 | 110 | ATP, CA |
| 3 | 649 | 0.82 | 0.87 | 91 | ATP, CA |
| 4 | 312 | 0.80 | 0.91 | 49 | ATP, CA |
| 5 | 54 | 0.72 | 0.98 | 20 | empty |
Interfaces
5 interfaces between chains.
- B–D · 1595 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 1567 Ų buried · 10 hydrogen bonds · protein-protein
- C–D · 838 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 800 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 460 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 3QB0 · Crystal structure of Actin-related protein Arp4 from S. cerevisiae complexed with ATP · the same entry in another collection · chain D against D, TM-score 1.00
- P80428 · AlphaFold monomer V2.0 prediction for actin-related protein 4 (P80428) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 P80428
- Elsewhere: RCSB PDB 3QB0 · PDBe 3QB0 · UniProt P80428
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