MolNFT v1 · #93694 · protein
Crystal structure of PLK1 polo-box domain in complex with pl-49
4HAB · SERINE/THREONINE-protein kinase PLK1: “Crystal structure of PLK1 polo-box domain in complex with pl-49”. X-ray diffraction, 2 ligands (NH2, PO4), 10 pockets (best druggability 0.66). MolNFT v1 #93694 on GenesisL1: 3D structure…
- PDB
- 4HAB
- Type
- protein
- Length
- 646 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- SERINE/THREONINE-protein kinase PLK1; Pl-49
- EC
- 2.7.11.21
- UniProt
- P53350
- Ligands
- NH2, PO4
- Pockets
- 10 · best druggability 0.66
Structure
x-ray diffraction · 4 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 | 223 | 30% helix, 29% strand | P53350 |
| B | SERINE/THREONINE-protein kinase PLK1 (EC 2.7.11.21) | protein | 218 | 28% helix, 30% strand | P53350 |
| C | SERINE/THREONINE-protein kinase PLK1 (EC 2.7.11.21) | protein | 187 | 26% helix, 26% strand | P53350 |
| D, E, F | Pl-49 | protein | 6 | 0% helix, 17% strand | — |
Ligands and binding sites
- NH2 · Amino group · ion · 3 copies · chains A, D, B, E, C, F
- PO4 · Phosphate ion · ion · chains A, C
- CXS · 3-cyclohexyl-1-propylsulfonic acid · additive · 5 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 411 | 0.66 | 0.79 | 47 | empty |
| 2 | 138 | 0.60 | 0.84 | 27 | empty |
| 3 | 61 | 0.50 | 0.85 | 13 | empty |
| 4 | 198 | 0.50 | 0.76 | 22 | PO4 |
| 5 | 61 | 0.48 | 0.85 | 19 | empty |
Interfaces
7 interfaces between chains.
- A–B · 534 Ų buried · 8 hydrogen bonds · protein-protein
- C–F · 522 Ų buried · 9 hydrogen bonds · protein-protein
- B–E · 521 Ų buried · 10 hydrogen bonds · protein-protein
- A–D · 516 Ų buried · 10 hydrogen bonds · protein-protein
- A–E · 284 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 modified (nonstandard, phosphorylation).
Compared structures
- 4HAB · Crystal structure of Plk1 Polo-box domain in complex with PL-49 · 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 4HAB · PDBe 4HAB · UniProt P53350
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