MolNFT v1 · #74653 · protein
Polo-like kinase I polo-box domain in complex with fdpplhspta phosphopeptide from PBIP1
3P37 · SERINE/THREONINE-protein kinase PLK1: “Polo-like kinase I polo-box domain in complex with fdpplhspta phosphopeptide from PBIP1”. X-ray diffraction, 2 ligands (ACE, NH2), 3 pockets (best druggability 0.80). MolNFT v1 #74653 on…
- PDB
- 3P37
- Type
- protein
- Length
- 690 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- SERINE/THREONINE-protein kinase PLK1; Phosphopeptide
- EC
- 2.7.11.21
- UniProt
- P53350
- Ligands
- ACE, NH2
- Pockets
- 3 · best druggability 0.80
Structure
x-ray diffraction · 4 distinct chains · 30% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | SERINE/THREONINE-protein kinase PLK1 (EC 2.7.11.21) | protein | 224 | 32% helix, 29% strand | P53350 |
| B | SERINE/THREONINE-protein kinase PLK1 (EC 2.7.11.21) | protein | 219 | 29% helix, 29% strand | P53350 |
| C | SERINE/THREONINE-protein kinase PLK1 (EC 2.7.11.21) | protein | 220 | 30% helix, 29% strand | P53350 |
| E, D, F | Phosphopeptide | protein | 9 | 0% helix, 22% strand | — |
Ligands and binding sites
- ACE · Acetyl group · ligand · 3 copies · chains A, E, B, D, F
- NH2 · Amino group · ion · chains B, D
- GOL · Glycerol · additive · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 869 | 0.80 | 0.83 | 96 | empty |
| 2 | 82 | 0.50 | 0.84 | 18 | empty |
| 3 | 81 | 0.35 | 0.75 | 24 | empty |
Interfaces
7 interfaces between chains.
- A–E · 690 Ų buried · 14 hydrogen bonds · protein-protein
- C–F · 677 Ų buried · 11 hydrogen bonds · protein-protein
- B–D · 662 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 337 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 273 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 covalent, 3 modified (covalent ligand, phosphorylation).
Compared structures
- 3P37 · Polo-like kinase I Polo-box domain in complex with FDPPLHSpTA phosphopeptide from PBIP1 · 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 3P37 · PDBe 3P37 · UniProt P53350
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