MolNFT v1 · #66168 · protein
Structure of human PLK1-pbd with glycerol and sulfate in the phophopeptide binding site
3HIH · SERINE/THREONINE-protein kinase PLK1: “Structure of human PLK1-pbd with glycerol and sulfate in the phophopeptide binding site”. X-ray diffraction, 1 ligand (SO4), 5 pockets (best druggability 0.67). MolNFT v1 #66168 on GenesisL1…
- PDB
- 3HIH
- Type
- protein
- Length
- 436 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- SERINE/THREONINE-protein kinase PLK1
- EC
- 2.7.11.21
- UniProt
- P53350
- Ligands
- SO4
- Pockets
- 5 · best druggability 0.67
Structure
x-ray diffraction · 2 distinct chains · 31% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | SERINE/THREONINE-protein kinase PLK1 (EC 2.7.11.21) | protein | 223 | 32% helix, 29% strand | P53350 |
| B | SERINE/THREONINE-protein kinase PLK1 (EC 2.7.11.21) | protein | 213 | 31% helix, 30% strand | P53350 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 5 copies · chains A, B
- GOL · Glycerol · additive · 5 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 423 | 0.67 | 0.80 | 49 | SO4, GOL |
| 2 | 158 | 0.47 | 0.76 | 23 | SO4, GOL |
| 3 | 126 | 0.42 | 0.75 | 26 | SO4 |
| 4 | 85 | 0.37 | 0.77 | 27 | GOL |
| 5 | 67 | 0.31 | 0.74 | 10 | empty |
Interfaces
1 interface between chains.
- A–B · 372 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 3HIH · Structure of human Plk1-PBD with glycerol and sulfate in the phophopeptide binding site · 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 3HIH · PDBe 3HIH · UniProt P53350
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