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Crystal structure of ARP2/3 complex with bound ATP and calcium
Analyse Crystal structure of ARP2/3 complex with bound ATP and calcium in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1TYQ
- Type
- protein
- Length
- 1,692 residues
- Chains
- 7
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Actin-related protein 3; Actin-related protein 2; ARP2/3 complex 41KDA subunit; ARP2/3…
- UniProt
- P61157
- Ligands
- ATP, CA
- Pockets
- 18 · best druggability 0.83
Structure
x-ray diffraction · 7 distinct chains · 38% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Actin-related protein 3 | protein | 399 | 45% helix, 20% strand | P61157 |
| B | Actin-related protein 2 | protein | 208 | 44% helix, 14% strand | — |
| C | ARP2/3 complex 41KDA subunit | protein | 342 | 3% helix, 51% strand | — |
| D | ARP2/3 complex 34KDA subunit | protein | 274 | 45% helix, 22% strand | — |
| E | ARP2/3 complex 21KDA subunit | protein | 169 | 47% helix, 6% strand | — |
| F | ARP2/3 complex 20KDA subunit | protein | 166 | 49% helix, 16% strand | — |
| G | ARP2/3 complex 16KDA subunit | protein | 134 | 65% helix, 0% strand | — |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 2 copies · chains A, B
- CA · Calcium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 688 | 0.83 | 0.87 | 70 | empty |
| 2 | 249 | 0.78 | 0.91 | 43 | empty |
| 3 | 100 | 0.77 | 0.97 | 24 | empty |
| 4 | 880 | 0.75 | 0.79 | 86 | ATP |
| 5 | 368 | 0.72 | 0.84 | 53 | CA, ATP |
Interfaces
12 interfaces between chains.
- D–F · 2209 Ų buried · 9 hydrogen bonds · protein-protein
- A–D · 1714 Ų buried · 26 hydrogen bonds · protein-protein
- C–F · 1212 Ų buried · 16 hydrogen bonds · protein-protein
- F–G · 953 Ų buried · 9 hydrogen bonds · protein-protein
- A–E · 919 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
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 P61157
- Elsewhere: RCSB PDB 1TYQ · PDBe 1TYQ · UniProt P61157
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