MolNFT v2 · #117033 · protein
Polo-box domain of Mouse Polo-like kinase 1 complexed with Emi2 (146-177)
5DMV · Serine/threonine-protein kinase PLK1: “Polo-box domain of Mouse Polo-like kinase 1 complexed with Emi2 (146-177)”. X-ray diffraction at 2.499, 1 ligand (NI), 3 pockets (best druggability 0.44). MolNFT v2 #117033 on GenesisL1: 3D…
- PDB
- 5DMV
- Type
- protein
- Length
- 241 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.499
- Source
- Mus musculus; SYNTHETIC CONSTRUCT
- Molecule
- Serine/threonine-protein kinase PLK1; F-box only protein 43
- EC
- 2.7.11.21
- UniProt
- Q07832, Q8CDI2
- Ligands
- NI
- Pockets
- 3 · best druggability 0.44
Structure
x-ray diffraction · resolution 2.499 · 2 distinct chains · 27% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | Serine/threonine-protein kinase PLK1 (EC 2.7.11.21) | protein | 230 | 28% helix, 28% strand | Q07832 |
| D | F-box only protein 43 | protein | 11 | 0% helix, 18% strand | Q8CDI2 |
Ligands and binding sites
- NI · Nickel (II) ion · metal · 3 copies · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 113 | 0.44 | 0.78 | 21 | empty |
| 2 | 119 | 0.39 | 0.75 | 19 | empty |
| 3 | 50 | 0.26 | 0.73 | 18 | empty |
Interfaces
1 interface between chains.
- C–D · 780 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (phosphorylation).
Compared structures
- 5DMV · Polo-box domain of mouse polo-like kinase 1 complexed with EMI2 (146- 177) · the same entry in another collection · chain C against C, TM-score 1.00
- Q07832 · AlphaFold monomer V2.0 prediction for SERINE/THREONINE-protein kinase PLK1 (Q07832) · a predicted model of the same protein · chain C against A, TM-score 0.92
- Q8CDI2 · AlphaFold monomer V2.0 prediction for F-box only protein 43 (Q8CDI2) · a predicted model of the same protein · chain D against A, TM-score 0.25
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 Q07832
- Every structure of UniProt Q8CDI2
- Elsewhere: RCSB PDB 5DMV · PDBe 5DMV · UniProt Q07832 · UniProt Q8CDI2
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