Research workbench
Crystal structure of bos taurus ARP2/3 complex with bound inhibitor ck-666
Analyse Crystal structure of bos taurus ARP2/3 complex with bound inhibitor ck-666 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3UKR
- Type
- protein
- Length
- 1,701 residues
- Chains
- 7
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Actin-related protein 3; Actin-related protein 2; Actin-related protein 2/3 complex…
- UniProt
- P61157, A7MB62, Q58CQ2, Q3MHR7, Q3T035, Q148J6, Q3SYX9
- Ligands
- CKH
- Pockets
- 20 · best druggability 0.84
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 | 401 | 43% helix, 19% strand | P61157 |
| B | Actin-related protein 2 | protein | 193 | 44% helix, 16% strand | A7MB62 |
| C | Actin-related protein 2/3 complex subunit 1B | protein | 349 | 5% helix, 50% strand | Q58CQ2 |
| D | Actin-related protein 2/3 complex subunit 2 | protein | 282 | 45% helix, 22% strand | Q3MHR7 |
| E | Actin-related protein 2/3 complex subunit 3 | protein | 173 | 48% helix, 6% strand | Q3T035 |
| F | Actin-related protein 2/3 complex subunit 4 | protein | 167 | 51% helix, 17% strand | Q148J6 |
| G | Actin-related protein 2/3 complex subunit 5 | protein | 136 | 62% helix, 0% strand | Q3SYX9 |
Ligands and binding sites
- CKH · 2-fluoro-N-[2-(2-methyl-1H-indol-3-yl)ethyl]benzamide · ligand · 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, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1134 | 0.84 | 0.85 | 109 | empty |
| 2 | 103 | 0.79 | 0.98 | 22 | empty |
| 3 | 336 | 0.77 | 0.88 | 50 | CKH |
| 4 | 539 | 0.73 | 0.81 | 48 | empty |
| 5 | 585 | 0.72 | 0.80 | 54 | empty |
Interfaces
12 interfaces between chains.
- D–F · 2207 Ų buried · 8 hydrogen bonds · protein-protein
- A–D · 1788 Ų buried · 28 hydrogen bonds · protein-protein
- C–F · 1178 Ų buried · 14 hydrogen bonds · protein-protein
- F–G · 929 Ų buried · 8 hydrogen bonds · protein-protein
- A–E · 922 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 3UKR · Crystal structure of Bos taurus Arp2/3 complex with bound inhibitor CK-666 · 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 3UKR · PDBe 3UKR · UniProt P61157 · UniProt A7MB62 · UniProt Q58CQ2 · UniProt Q3MHR7 · UniProt Q3T035 · UniProt Q148J6 · UniProt Q3SYX9
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