Research workbench
The polo-box domain of PLK1 in complex with a phospho- peptide
Analyse The polo-box domain of PLK1 in complex with a phospho- peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1Q4K
- Type
- protein
- Length
- 678 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- SERINE/THREONINE-protein kinase plk; Phospho-peptide sequence MET.GLN.SER.PTHR.PRO.LEU
- EC
- 2.7.1.-
- UniProt
- P53350
- Pockets
- 6 · best druggability 0.63
Structure
x-ray diffraction · 4 distinct chains · 30% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | SERINE/THREONINE-protein kinase plk (EC 2.7.1.-) | protein | 224 | 30% helix, 29% strand | P53350 |
| A | SERINE/THREONINE-protein kinase plk (EC 2.7.1.-) | protein | 222 | 30% helix, 30% strand | P53350 |
| C | SERINE/THREONINE-protein kinase plk (EC 2.7.1.-) | protein | 214 | 30% helix, 30% strand | P53350 |
| D, E, F | Phospho-peptide sequence MET.GLN.SER.PTHR.PRO.LEU | protein | 6 | 0% helix, 33% strand | — |
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 63 | 0.63 | 0.92 | 21 | empty |
| 2 | 512 | 0.61 | 0.75 | 39 | empty |
| 3 | 438 | 0.61 | 0.76 | 45 | empty |
| 4 | 131 | 0.48 | 0.79 | 26 | empty |
| 5 | 121 | 0.44 | 0.77 | 23 | empty |
Interfaces
6 interfaces between chains.
- B–E · 553 Ų buried · 10 hydrogen bonds · protein-protein
- C–F · 540 Ų buried · 12 hydrogen bonds · protein-protein
- A–D · 538 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 438 Ų buried · 5 hydrogen bonds · protein-protein
- B–A · 429 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 modified (phosphorylation).
Compared structures
- 1Q4K · The polo-box domain of Plk1 in complex with a phospho-peptide · the same entry in another collection · chain F against F, TM-score 1.00
- P53350 · AlphaFold monomer V2.0 prediction for SERINE/THREONINE-protein kinase PLK1 (P53350) · a predicted model of the same protein · chain C against A, TM-score 0.96
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
- Elsewhere: RCSB PDB 1Q4K · PDBe 1Q4K · UniProt P53350
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