Research workbench
Crystal structure of fission yeast ARP2/3 complex lacking the ARP2 subunit
Analyse Crystal structure of fission yeast ARP2/3 complex lacking the ARP2 subunit in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3DWL
- Type
- protein
- Length
- 2,613 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Actin-related protein 3; Actin-related protein 2/3 complex subunit 1; Actin-related…
- UniProt
- P32390, P78774, O14241, Q9Y7J4, Q92352, Q10316
- Ligands
- ATP
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 7 distinct chains · 27% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Actin-related protein 3 | protein | 355 | 42% helix, 15% strand | P32390 |
| C | Actin-related protein 2/3 complex subunit 1 | protein | 336 | 0% helix, 43% strand | P78774 |
| D, I | Actin-related protein 2/3 complex subunit 2 | protein | 272 | 40% helix, 17% strand | O14241 |
| E, J | Actin-related protein 2/3 complex subunit 3 | protein | 63 | 49% helix, 0% strand | Q9Y7J4 |
| F, K | Actin-related protein 2/3 complex subunit 4 | protein | 166 | 46% helix, 16% strand | Q92352 |
| G, L | Actin-related protein 2/3 complex subunit 5 | protein | 114 | 68% helix, 0% strand | Q10316 |
| H | Actin-related protein 2/3 complex subunit 1 | protein | 337 | 0% helix, 45% strand | P78774 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · 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, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1062 | 0.84 | 0.85 | 101 | empty |
| 2 | 1060 | 0.84 | 0.84 | 107 | empty |
| 3 | 747 | 0.75 | 0.80 | 82 | empty |
| 4 | 1079 | 0.75 | 0.78 | 95 | ATP |
| 5 | 966 | 0.75 | 0.78 | 87 | empty |
Interfaces
22 interfaces between chains.
- I–K · 2032 Ų buried · 9 hydrogen bonds · protein-protein
- D–F · 2024 Ų buried · 10 hydrogen bonds · protein-protein
- B–I · 1519 Ų buried · 24 hydrogen bonds · protein-protein
- A–D · 1503 Ų buried · 23 hydrogen bonds · protein-protein
- H–K · 957 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 3DWL · Crystal Structure of Fission Yeast Arp2/3 Complex Lacking the Arp2 Subunit · the same entry in another collection · chain L against L, 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 P32390
- Every structure of UniProt P78774
- Every structure of UniProt O14241
- Every structure of UniProt Q9Y7J4
- Every structure of UniProt Q92352
- Every structure of UniProt Q10316
- Elsewhere: RCSB PDB 3DWL · PDBe 3DWL · UniProt P32390 · UniProt P78774 · UniProt O14241 · UniProt Q9Y7J4 · UniProt Q92352 · UniProt Q10316
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