Research workbench
CDC7-DBF4 bound to ADP-BEF3
Analyse CDC7-DBF4 bound to ADP-BEF3 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6YA8
- Type
- protein
- Length
- 443 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cell division cycle 7-related protein KINASE,CELL division cycle 7-related protein…
- EC
- 2.7.11.1
- UniProt
- O00311, Q9UBU7
- Ligands
- ADP, BEF, MG, ZN
- Pockets
- 2 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cell division cycle 7-related protein KINASE,CELL division cycle 7-related protein KINASE,CELL division cycle 7-related protein kinase (EC 2.7.11.1) | protein | 340 | 42% helix, 17% strand | O00311 |
| B | Protein DBF4 homolog a | protein | 103 | 18% helix, 18% strand | Q9UBU7 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · chains A
- BEF · Beryllium trifluoride ion · ligand · chains A
- MG · Magnesium ion · metal · 2 copies · chains A
- ZN · Zinc ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 446 | 0.69 | 0.80 | 55 | ADP, MG, BEF |
| 2 | 397 | 0.61 | 0.77 | 34 | empty |
Interfaces
1 interface between chains.
- A–B · 3745 Ų buried · 48 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (phosphorylation).
Compared structures
- 6YA8 · Cdc7-Dbf4 bound to ADP-BeF3 · the same entry in another collection · chain A against A, TM-score 1.00
- O00311 · AlphaFold monomer V2.0 prediction for cell division cycle 7-related protein kinase… · a predicted model of the same protein · chain A against A, TM-score 0.99
- Q9UBU7 · AlphaFold monomer V2.0 prediction for protein DBF4 homolog a (Q9UBU7) · a predicted model of the same protein · chain B against A, TM-score 0.93
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 O00311
- Every structure of UniProt Q9UBU7
- Elsewhere: RCSB PDB 6YA8 · PDBe 6YA8 · UniProt O00311 · UniProt Q9UBU7
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