MolNFT v1 · #109676 · protein
Plk-1 polo-box domain in complex with bioactive imidazolium-containing phosphopeptide macrocycle 4C
4X9W · SERINE/THREONINE-protein kinase PLK1: “Plk-1 polo-box domain in complex with bioactive imidazolium-containing phosphopeptide macrocycle 4C”. X-ray diffraction, 2 ligands (3ZH, NH2), 2 pockets (best druggability 0.45). MolNFT v1…
- PDB
- 4X9W
- Type
- protein
- Length
- 229 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- SERINE/THREONINE-protein kinase PLK1; Macrocyclic phosphopeptide 4C
- EC
- 2.7.11.21
- UniProt
- P53350
- Ligands
- 3ZH, NH2
- Pockets
- 2 · best druggability 0.45
Structure
x-ray diffraction · 2 distinct chains · 28% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | SERINE/THREONINE-protein kinase PLK1 (EC 2.7.11.21) | protein | 226 | 29% helix, 29% strand | P53350 |
| B | Macrocyclic phosphopeptide 4C | protein | 3 | 0% helix, 0% strand | — |
Ligands and binding sites
- 3ZH · 11-{4-[(2S)-2-amino-2-carboxyethyl]-3-(8-phenyloctyl)-2,3-dihydro-1H-imidazol-1-yl}undecanoic acid · ligand · chains A, B
- NH2 · Amino group · ion · chains A, B
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 | 123 | 0.45 | 0.78 | 25 | empty |
| 2 | 101 | 0.36 | 0.75 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 359 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent, 1 modified (covalent ligand, phosphorylation).
Compared structures
- 4X9W · PLK-1 polo-box domain in complex with Bioactive Imidazolium-containing phosphopeptide… · the same entry in another collection · chain B against B, 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 4X9W · PDBe 4X9W · UniProt P53350
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