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Crystal structure of budding yeast Cdc5 polo-box domain in complex with Spc72 phosphopeptide.
Analyse Crystal structure of budding yeast Cdc5 polo-box domain in complex with Spc72… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6MF5
- Type
- protein
- Length
- 526 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.7
- Source
- Saccharomyces cerevisiae
- Molecule
- Cell cycle serine/threonine-protein kinase CDC5/MSD2; Spc72
- EC
- 2.7.11.21
- UniProt
- P32562
- Ligands
- CL
- Pockets
- 7 · best druggability 0.68
Structure
x-ray diffraction · resolution 2.7 · 3 distinct chains · 31% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cell cycle serine/threonine-protein kinase CDC5/MSD2 (EC 2.7.11.21) | protein | 250 | 31% helix, 29% strand | P32562 |
| B | Cell cycle serine/threonine-protein kinase CDC5/MSD2 (EC 2.7.11.21) | protein | 262 | 32% helix, 26% strand | P32562 |
| C, D | Spc72 | protein | 7 | 0% helix, 43% strand | — |
Ligands and binding sites
- CL · Chloride ion · ion · 2 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 414 | 0.68 | 0.80 | 47 | empty |
| 2 | 265 | 0.53 | 0.76 | 38 | empty |
| 3 | 90 | 0.49 | 0.82 | 19 | empty |
| 4 | 63 | 0.46 | 0.84 | 27 | empty |
| 5 | 119 | 0.43 | 0.77 | 19 | empty |
Interfaces
3 interfaces between chains.
- A–B · 902 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 492 Ų buried · 11 hydrogen bonds · protein-protein
- B–D · 461 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (phosphorylation).
Compared structures
- 6MF5 · Crystal structure of budding yeast CDC5 polo-box domain in complex with SPC72… · the same entry in another collection · chain A against A, TM-score 1.00
- P32562 · AlphaFold monomer V2.0 prediction for cell cycle SERINE/THREONINE- protein kinase… · a predicted model of the same protein · chain B against A, TM-score 0.97
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 P32562
- Elsewhere: RCSB PDB 6MF5 · PDBe 6MF5 · UniProt P32562
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