MolNFT v1 · #88961 · protein
Crystal structure of PAK1 kinase domain with the ruthenium phthalimide complex
4DAW · SERINE/THREONINE-protein kinase pak 1: “Crystal structure of PAK1 kinase domain with the ruthenium phthalimide complex”. X-ray diffraction, 1 ligand (0H2), 3 pockets (best druggability 0.61). MolNFT v1 #88961 on GenesisL1: 3D…
- PDB
- 4DAW
- Type
- protein
- Length
- 294 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- SERINE/THREONINE-protein kinase pak 1
- EC
- 2.7.11.1
- UniProt
- Q13153
- Ligands
- 0H2
- Pockets
- 3 · best druggability 0.61
Structure
x-ray diffraction · 1 distinct chain · 44% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | SERINE/THREONINE-protein kinase pak 1 (EC 2.7.11.1) | protein | 294 | 44% helix, 19% strand | Q13153 |
Ligands and binding sites
- 0H2 · [1,3-dioxo-6-(pyridin-2-yl-kappaN)-2,3-dihydro-1H-isoindol-5-yl-kappaC~5~][(thioxomethylidene)azanido-kappaN](1,4,7-trithionane-kappa~3~S~1~,S~4~,S~7~)ruthenium · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 312 | 0.61 | 0.78 | 36 | 0H2 |
| 2 | 111 | 0.47 | 0.79 | 14 | empty |
| 3 | 62 | 0.28 | 0.73 | 17 | empty |
Modifications
Observed in the structure: 1 modified (phosphorylation).
Compared structures
- 4DAW · Crystal structure of PAK1 kinase domain with the ruthenium phthalimide complex · the same entry in another collection · chain A against A, TM-score 1.00
- Q13153 · AlphaFold monomer V2.0 prediction for SERINE/THREONINE-protein kinase pak 1 (Q13153) · a predicted model of the same protein · chain A 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 Q13153
- Elsewhere: RCSB PDB 4DAW · PDBe 4DAW · UniProt Q13153
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