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The structure of the polo-box domain (pbd) of polo-like kinase 1 (PLK1) in complex with 3-(1-benzothiophen-2-YL)PROPANOYL-derivatized dpplhspta peptide
Analyse The structure of the polo-box domain (pbd) of polo-like kinase 1 (PLK1) in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4E9D
- Type
- protein
- Length
- 230 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- SERINE/THREONINE-protein kinase PLK1; 3-(1-benzothiophen-2-YL)PROPANOYL-derivatized…
- EC
- 2.7.11.21
- UniProt
- P53350
- Ligands
- 0OB
- Pockets
- 2 · best druggability 0.43
Structure
x-ray diffraction · 2 distinct chains · 25% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | SERINE/THREONINE-protein kinase PLK1 (EC 2.7.11.21) | protein | 222 | 26% helix, 29% strand | P53350 |
| E | 3-(1-benzothiophen-2-YL)PROPANOYL-derivatized dpplhspta peptide | protein | 8 | 0% helix, 25% strand | — |
Ligands and binding sites
- 0OB · 3-(1-benzothiophen-2-yl)propanoic acid · ligand · chains A, E
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 63 | 0.43 | 0.82 | 14 | empty |
| 2 | 59 | 0.40 | 0.81 | 16 | empty |
Interfaces
1 interface between chains.
- A–E · 574 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent, 1 modified (covalent ligand, phosphorylation).
Compared structures
- 4E9D · The structure of the polo-box domain (PBD) of polo-like kinase 1 (Plk1) in complex with… · 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
- Elsewhere: RCSB PDB 4E9D · PDBe 4E9D · UniProt P53350
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