MolNFT v1 · #89120 · protein
Oxime-based post solid-phase peptide diversification: identification of high affinity polo-like kinase 1 (PLK1) polo-box domain binding peptides
4DFW · SERINE/THREONINE-protein kinase PLK1: “Oxime-based post solid-phase peptide diversification: identification of high affinity polo-like kinase 1…”. X-ray diffraction, 3 ligands (ACE, CL, NH2), 2 pockets (best druggability 0.38).…
- PDB
- 4DFW
- Type
- protein
- Length
- 224 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- SERINE/THREONINE-protein kinase PLK1; Peptide
- EC
- 2.7.11.21
- UniProt
- P53350
- Ligands
- ACE, CL, NH2
- Pockets
- 2 · best druggability 0.38
Structure
x-ray diffraction · 2 distinct chains · 29% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | SERINE/THREONINE-protein kinase PLK1 (EC 2.7.11.21) | protein | 219 | 30% helix, 30% strand | P53350 |
| D | Peptide | protein | 5 | 0% helix, 40% strand | — |
Ligands and binding sites
- ACE · Acetyl group · ligand · chains D
- CL · Chloride ion · ion · 2 copies · chains A
- NH2 · Amino group · ion · chains A, D
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 | 66 | 0.38 | 0.79 | 19 | empty |
| 2 | 73 | 0.29 | 0.73 | 15 | empty |
Interfaces
1 interface between chains.
- A–D · 627 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified, 1 covalent (covalent ligand, nonstandard, phosphorylation).
Compared structures
- 4DFW · Oxime-based Post Solid-phase Peptide Diversification: Identification of High Affinity… · 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 4DFW · PDBe 4DFW · UniProt P53350
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