Research workbench
Crystal structures of the phosphorylated and unphosphorylated kinase domains of the CDC42-associated tyrosine kinase ACK1 bound to AMP-pcp
Analyse Crystal structures of the phosphorylated and unphosphorylated kinase domains of… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1U54
- Type
- protein
- Length
- 524 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Activated CDC42 kinase 1
- EC
- 2.7.1.112
- UniProt
- Q07912
- Ligands
- ACP, MG
- Pockets
- 6 · best druggability 0.64
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Activated CDC42 kinase 1 (EC 2.7.1.112) | protein | 263 | 39% helix, 18% strand | Q07912 |
| B | Activated CDC42 kinase 1 (EC 2.7.1.112) | protein | 261 | 39% helix, 20% strand | Q07912 |
Ligands and binding sites
- ACP · Phosphomethylphosphonic acid adenylate ester · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 420 | 0.64 | 0.78 | 43 | MG, ACP |
| 2 | 345 | 0.63 | 0.79 | 40 | MG, ACP |
| 3 | 370 | 0.61 | 0.77 | 47 | empty |
| 4 | 131 | 0.52 | 0.80 | 31 | empty |
| 5 | 117 | 0.38 | 0.75 | 20 | MG |
Interfaces
1 interface between chains.
- A–B · 653 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (phosphorylation).
Compared structures
- 1U54 · Crystal Structures of the Phosphorylated and Unphosphorylated Kinase Domains of the… · the same entry in another collection · chain A against A, TM-score 1.00
- Q07912 · AlphaFold monomer V2.0 prediction for activated CDC42 kinase 1 (Q07912) · a predicted model of the same protein · chain B against A, TM-score 0.96
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 Q07912
- Elsewhere: RCSB PDB 1U54 · PDBe 1U54 · UniProt Q07912
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