Research workbench
Polo-like kinase I polo-box domain in complex with mqspspl phosphopeptide
Analyse Polo-like kinase I polo-box domain in complex with mqspspl phosphopeptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3P35
- Type
- protein
- Length
- 673 residues
- Chains
- 5
- 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
- 7 · best druggability 0.77
Structure
x-ray diffraction · 3 distinct chains · 30% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | SERINE/THREONINE-protein kinase PLK1 (EC 2.7.11.21) | protein | 217 | 30% helix, 30% strand | P53350 |
| B, C | SERINE/THREONINE-protein kinase PLK1 (EC 2.7.11.21) | protein | 222 | 30% helix, 30% strand | P53350 |
| D, E | Phosphopeptide | protein | 6 | 0% helix, 33% strand | — |
Ligands and binding sites
- ACE · Acetyl group · ligand · 2 copies · chains A, D, B, E
- NH2 · Amino group · ion · 2 copies · chains A, D, B, E
- GOL · Glycerol · additive · 5 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1190 | 0.77 | 0.79 | 109 | NH2, GOL |
| 2 | 160 | 0.48 | 0.77 | 26 | empty |
| 3 | 152 | 0.42 | 0.74 | 29 | empty |
| 4 | 50 | 0.39 | 0.82 | 17 | empty |
| 5 | 65 | 0.35 | 0.77 | 17 | empty |
Interfaces
7 interfaces between chains.
- A–D · 539 Ų buried · 13 hydrogen bonds · protein-protein
- B–E · 533 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 405 Ų buried · 3 hydrogen bonds · protein-protein
- A–E · 273 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 265 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent, 2 modified (covalent ligand, phosphorylation).
Compared structures
- 3P35 · Polo-like kinase I Polo-box domain in complex with MQSpSPL phosphopeptide · 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 3P35 · PDBe 3P35 · UniProt P53350
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