Research workbench
Crystal structure of polo box domain in complex with cyclic peptide inhibitor
Analyse Crystal structure of polo box domain in complex with cyclic peptide inhibitor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7MSO
- Type
- protein
- Length
- 445 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- SERINE/THREONINE-protein kinase PLK1; Cyclic peptide inhibitor ZO1-gln-ser-tpo-45W-mll
- EC
- 2.7.11.21
- UniProt
- P53350
- Ligands
- ZO1
- Pockets
- 4 · best druggability 0.40
Structure
x-ray diffraction · 3 distinct chains · 32% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | SERINE/THREONINE-protein kinase PLK1 (EC 2.7.11.21) | protein | 214 | 32% helix, 31% strand | P53350 |
| B | SERINE/THREONINE-protein kinase PLK1 (EC 2.7.11.21) | protein | 221 | 33% helix, 30% strand | P53350 |
| E, F | Cyclic peptide inhibitor ZO1-gln-ser-tpo-45W-mll | protein | 5 | 0% helix, 20% strand | — |
Ligands and binding sites
- ZO1 · 3-(trifluoromethyl)benzaldehyde · ligand · 2 copies · chains A, E, B, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 97 | 0.40 | 0.76 | 25 | empty |
| 2 | 54 | 0.33 | 0.77 | 15 | empty |
| 3 | 67 | 0.33 | 0.75 | 13 | empty |
| 4 | 63 | 0.33 | 0.76 | 13 | empty |
Interfaces
3 interfaces between chains.
- B–F · 460 Ų buried · 9 hydrogen bonds · protein-protein
- A–E · 452 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 13 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 modified, 2 covalent (nonstandard, covalent ligand, phosphorylation).
Compared structures
- 7MSO · Crystal Structure of Polo Box Domain in Complex with Cyclic Peptide Inhibitor · 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 7MSO · PDBe 7MSO · UniProt P53350
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