Research workbench
Crystal structure of budding yeast CDC5 polo-box domain in complex with the DBF4 polo-interacting region.
Analyse Crystal structure of budding yeast CDC5 polo-box domain in complex with the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6MF6
- Type
- protein
- Length
- 501 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cell cycle SERINE/THREONINE-protein kinase CDC5/MSD2; Ddk kinase regulatory subunit DBF4
- EC
- 2.7.11.21
- UniProt
- P32562, P32325
- Pockets
- 9 · best druggability 0.77
Structure
x-ray diffraction · 4 distinct chains · 28% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cell cycle SERINE/THREONINE-protein kinase CDC5/MSD2 (EC 2.7.11.21) | protein | 244 | 29% helix, 27% strand | P32562 |
| B | Cell cycle SERINE/THREONINE-protein kinase CDC5/MSD2 (EC 2.7.11.21) | protein | 239 | 29% helix, 27% strand | P32562 |
| D | Ddk kinase regulatory subunit DBF4 | protein | 10 | 0% helix, 20% strand | P32325 |
| C | Ddk kinase regulatory subunit DBF4 | protein | 8 | 0% helix, 13% strand | P32325 |
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1053 | 0.77 | 0.79 | 78 | empty |
| 2 | 71 | 0.71 | 0.96 | 23 | empty |
| 3 | 50 | 0.61 | 0.92 | 17 | empty |
| 4 | 82 | 0.54 | 0.85 | 21 | empty |
| 5 | 130 | 0.47 | 0.78 | 26 | empty |
Interfaces
3 interfaces between chains.
- A–B · 767 Ų buried · 4 hydrogen bonds · protein-protein
- B–D · 553 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 477 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 6MF6 · Crystal structure of budding yeast Cdc5 polo-box domain in complex with the Dbf4… · the same entry in another collection · chain C against C, 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 0.95
- P32325 · AlphaFold monomer V2.0 prediction for ddk kinase regulatory subunit DBF4 (P32325) · a predicted model of the same protein · chain C against A, TM-score 0.41
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
- Every structure of UniProt P32325
- Elsewhere: RCSB PDB 6MF6 · PDBe 6MF6 · UniProt P32562 · UniProt P32325
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.