Research workbench
Human CDC7 kinase in complex with DBF4 and nucleotide
Analyse Human CDC7 kinase in complex with DBF4 and nucleotide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4F9A
- Type
- protein
- Length
- 812 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cell division cycle 7-related protein kinase; Protein DBF4 homolog a
- EC
- 2.7.11.1
- UniProt
- O00311, Q9UBU7
- Ligands
- ADP, MG, ZN
- Pockets
- 10 · best druggability 0.64
Structure
x-ray diffraction · 3 distinct chains · 39% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cell division cycle 7-related protein kinase (EC 2.7.11.1) | protein | 315 | 42% helix, 18% strand | O00311 |
| B, D | Protein DBF4 homolog a | protein | 90 | 21% helix, 17% strand | Q9UBU7 |
| C | Cell division cycle 7-related protein kinase (EC 2.7.11.1) | protein | 317 | 42% helix, 18% strand | O00311 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, C
- MG · Magnesium ion · metal · 2 copies · chains A, C
- ZN · Zinc ion · metal · 2 copies · chains B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 267 | 0.64 | 0.81 | 36 | ADP, MG |
| 2 | 249 | 0.63 | 0.81 | 40 | ADP, MG |
| 3 | 188 | 0.55 | 0.80 | 27 | empty |
| 4 | 220 | 0.52 | 0.77 | 31 | empty |
| 5 | 215 | 0.52 | 0.77 | 29 | empty |
Interfaces
5 interfaces between chains.
- A–B · 3042 Ų buried · 33 hydrogen bonds · protein-protein
- C–D · 2975 Ų buried · 30 hydrogen bonds · protein-protein
- A–C · 148 Ų buried · 0 hydrogen bonds · protein-protein
- A–D · 38 Ų buried · 0 hydrogen bonds · protein-protein
- B–C · 19 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4F9A · Human CDC7 kinase in complex with DBF4 and nucleotide · the same entry in another collection · chain D against D, 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 C against A, TM-score 0.98
- Q9UBU7 · AlphaFold monomer V2.0 prediction for protein DBF4 homolog a (Q9UBU7) · a predicted model of the same protein · chain D against A, TM-score 0.94
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 4F9A · PDBe 4F9A · UniProt O00311 · UniProt Q9UBU7
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