MolNFT v1 · #91303 · protein
Human CDC7 kinase in complex with DBF4 and nucleotide
4F99 · Cell division cycle 7-related protein kinase: “Human CDC7 kinase in complex with DBF4 and nucleotide”. X-ray diffraction, 3 ligands (ADP, MG, ZN), 3 pockets (best druggability 0.67). MolNFT v1 #91303 on GenesisL1: 3D structure…
- PDB
- 4F99
- Type
- protein
- Length
- 402 residues
- Chains
- 2
- 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
- 3 · best druggability 0.67
Structure
x-ray diffraction · 2 distinct chains · 38% 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 | 312 | 41% helix, 18% strand | O00311 |
| B | Protein DBF4 homolog a | protein | 90 | 24% helix, 17% strand | Q9UBU7 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · chains A
- MG · Magnesium ion · metal · chains A
- ZN · Zinc ion · metal · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 289 | 0.67 | 0.82 | 42 | ADP, MG |
| 2 | 225 | 0.50 | 0.76 | 29 | empty |
| 3 | 69 | 0.36 | 0.77 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 3017 Ų buried · 31 hydrogen bonds · protein-protein
Compared structures
- 4F99 · Human CDC7 kinase in complex with DBF4 and nucleotide · 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 0.94
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 4F99 · PDBe 4F99 · UniProt O00311 · UniProt Q9UBU7
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