Research workbench
Crystal structure of the human LIMK1 kinase domain in complex with staurosporine
Analyse Crystal structure of the human LIMK1 kinase domain in complex with staurosporine in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3S95
- Type
- protein
- Length
- 580 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lim domain kinase 1
- EC
- 2.7.11.1
- UniProt
- P53667
- Ligands
- STU, NA, CL
- Pockets
- 5 · best druggability 0.65
Structure
x-ray diffraction · 1 distinct chain · 41% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Lim domain kinase 1 (EC 2.7.11.1) | protein | 290 | 41% helix, 19% strand | P53667 |
Ligands and binding sites
- STU · Staurosporine · ligand · 2 copies · chains A, B
- NA · Sodium ion · metal · 2 copies · chains A, B
- CL · Chloride ion · ion · 2 copies · chains A, B
- GOL · Glycerol · additive · 11 copies · chains A, B
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · 2 copies · chains A, B
- MRD · (4R)-2-methylpentane-2,4-diol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 339 | 0.65 | 0.80 | 38 | STU |
| 2 | 390 | 0.62 | 0.77 | 41 | GOL |
| 3 | 291 | 0.61 | 0.79 | 35 | STU |
| 4 | 152 | 0.50 | 0.78 | 23 | CL |
| 5 | 148 | 0.42 | 0.75 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 449 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 3S95 · Crystal structure of the human LIMK1 kinase domain in complex with staurosporine · the same entry in another collection · chain A against A, TM-score 1.00
- P53667 · AlphaFold monomer V2.0 prediction for lim domain kinase 1 (P53667) · 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 P53667
- Elsewhere: RCSB PDB 3S95 · PDBe 3S95 · UniProt P53667
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