Research workbench
Crystal structure of bovine ARP2/3 complex co-crystallized with AMP- pnp and calcium
Analyse Crystal structure of bovine ARP2/3 complex co-crystallized with AMP- pnp and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2P9U
- Type
- protein
- Length
- 1,698 residues
- Chains
- 7
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Actin-like protein 3; Actin-like protein 2; Actin-related protein 2/3 complex subunit 1B…
- UniProt
- P61157, A7MB62, Q58CQ2, Q3MHR7, Q3T035, Q148J6, Q3SYX9
- Ligands
- ANP, 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-like protein 3 | protein | 398 | 44% helix, 19% strand | P61157 |
| B | Actin-like protein 2 | protein | 222 | 44% helix, 14% strand | A7MB62 |
| C | Actin-related protein 2/3 complex subunit 1B | protein | 341 | 3% helix, 50% strand | Q58CQ2 |
| D | Actin-related protein 2/3 complex subunit 2 | protein | 280 | 44% helix, 22% strand | Q3MHR7 |
| E | Actin-related protein 2/3 complex subunit 3 | protein | 174 | 45% helix, 3% strand | Q3T035 |
| F | Actin-related protein 2/3 complex subunit 4 | protein | 167 | 49% helix, 16% strand | Q148J6 |
| G | Actin-related protein 2/3 complex subunit 5 | protein | 116 | 66% helix, 0% strand | Q3SYX9 |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · 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, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 688 | 0.83 | 0.87 | 69 | empty |
| 2 | 771 | 0.78 | 0.82 | 93 | empty |
| 3 | 98 | 0.77 | 0.97 | 23 | empty |
| 4 | 466 | 0.73 | 0.83 | 51 | CA, ANP |
| 5 | 579 | 0.70 | 0.79 | 69 | empty |
Interfaces
12 interfaces between chains.
- D–F · 2248 Ų buried · 14 hydrogen bonds · protein-protein
- A–D · 1762 Ų buried · 29 hydrogen bonds · protein-protein
- C–F · 1223 Ų buried · 15 hydrogen bonds · protein-protein
- F–G · 949 Ų buried · 7 hydrogen bonds · protein-protein
- A–E · 923 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 2P9U · Crystal structure of bovine Arp2/3 complex co-crystallized with AMP-PNP and calcium · the same entry in another collection · chain G against G, TM-score 1.00
- Q58CQ2 · AlphaFold monomer V2.0 prediction for actin-related protein 2/3 complex subunit 1B… · a predicted model of the same protein · chain C against A, TM-score 1.00
- Q3MHR7 · AlphaFold monomer V2.0 prediction for actin-related protein 2/3 complex subunit 2 (Q3MHR7) · a predicted model of the same protein · chain D against A, TM-score 0.99
- Q3T035 · AlphaFold monomer V2.0 prediction for actin-related protein 2/3 complex subunit 3 (Q3T035) · a predicted model of the same protein · chain E against A, TM-score 0.98
- Q3SYX9 · AlphaFold monomer V2.0 prediction for actin-related protein 2/3 complex subunit 5 (Q3SYX9) · a predicted model of the same protein · chain G against A, TM-score 0.98
- Q148J6 · AlphaFold monomer V2.0 prediction for actin-related protein 2/3 complex subunit 4 (Q148J6) · a predicted model of the same protein · chain F 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 P61157
- Every structure of UniProt A7MB62
- Every structure of UniProt Q58CQ2
- Every structure of UniProt Q3MHR7
- Every structure of UniProt Q3T035
- Every structure of UniProt Q148J6
- Every structure of UniProt Q3SYX9
- Elsewhere: RCSB PDB 2P9U · PDBe 2P9U · UniProt P61157 · UniProt A7MB62 · UniProt Q58CQ2 · UniProt Q3MHR7 · UniProt Q3T035 · UniProt Q148J6 · UniProt Q3SYX9
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