Research workbench
Crystal structure of the human P21-activated kinase 5
Analyse Crystal structure of the human P21-activated kinase 5 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2F57
- Type
- protein
- Length
- 598 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- SERINE/THREONINE-protein kinase pak 7
- EC
- 2.7.1.37
- UniProt
- Q9P286
- Ligands
- 23D
- Pockets
- 4 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | SERINE/THREONINE-protein kinase pak 7 (EC 2.7.1.37) | protein | 298 | 41% helix, 18% strand | Q9P286 |
| B | SERINE/THREONINE-protein kinase pak 7 (EC 2.7.1.37) | protein | 300 | 40% helix, 18% strand | Q9P286 |
Ligands and binding sites
- 23D · N2-[(1R,2S)-2-aminocyclohexyl]-N6-(3-chlorophenyl)-9-ethyl-9H-purine-2,6-diamine · ligand · chains B
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1102 | 0.78 | 0.80 | 112 | empty |
| 2 | 457 | 0.65 | 0.77 | 50 | TRS |
| 3 | 252 | 0.60 | 0.79 | 35 | 23D |
| 4 | 114 | 0.42 | 0.76 | 25 | empty |
Interfaces
1 interface between chains.
- A–B · 844 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (phosphorylation).
Compared structures
- 2F57 · Crystal Structure Of The Human P21-Activated Kinase 5 · the same entry in another collection · chain A against A, TM-score 1.00
- Q9P286 · AlphaFold monomer V2.0 prediction for SERINE/THREONINE-protein kinase pak 5 (Q9P286) · a predicted model of the same protein · chain B against A, TM-score 0.94
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 Q9P286
- Elsewhere: RCSB PDB 2F57 · PDBe 2F57 · UniProt Q9P286
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