Research workbench
Phospho-pon binding-induced PLK1 dimerization
Analyse Phospho-pon binding-induced PLK1 dimerization in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5J19
- Type
- protein
- Length
- 468 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- SERINE/THREONINE-protein kinase PLK1; Phosphorylated peptide from partner of numb
- EC
- 2.7.11.21
- UniProt
- P53350, O96561
- Pockets
- 5 · best druggability 0.56
Structure
x-ray diffraction · 4 distinct chains · 31% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | SERINE/THREONINE-protein kinase PLK1 (EC 2.7.11.21) | protein | 221 | 31% helix, 30% strand | P53350 |
| B | SERINE/THREONINE-protein kinase PLK1 (EC 2.7.11.21) | protein | 230 | 33% helix, 29% strand | P53350 |
| C | Phosphorylated peptide from partner of numb | protein | 9 | 0% helix, 22% strand | O96561 |
| D | Phosphorylated peptide from partner of numb | protein | 8 | 0% helix, 25% strand | O96561 |
Ligands and binding sites
- GOL · Glycerol · additive · 3 copies · chains A, 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 76 | 0.56 | 0.87 | 31 | empty |
| 2 | 127 | 0.52 | 0.81 | 23 | empty |
| 3 | 119 | 0.46 | 0.78 | 31 | empty |
| 4 | 77 | 0.39 | 0.78 | 16 | GOL |
| 5 | 86 | 0.33 | 0.74 | 17 | empty |
Interfaces
4 interfaces between chains.
- A–B · 841 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 606 Ų buried · 14 hydrogen bonds · protein-protein
- A–D · 584 Ų buried · 14 hydrogen bonds · protein-protein
- A–C · 78 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (phosphorylation).
Compared structures
- 5J19 · phospho-Pon binding-induced Plk1 dimerization · the same entry in another collection · chain A against A, TM-score 1.00
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 P53350
- Every structure of UniProt O96561
- Elsewhere: RCSB PDB 5J19 · PDBe 5J19 · UniProt P53350 · UniProt O96561
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