MolNFT v1 · #176818 · protein
Crystal structure of cyanobacterial circadian clock protein kaic
7DYJ · Circadian clock protein kinase kaic: “Crystal structure of cyanobacterial circadian clock protein kaic”. X-ray diffraction, 2 ligands (ATP, MG), 13 pockets (best druggability 0.78). MolNFT v1 #176818 on GenesisL1: 3D structure…
- PDB
- 7DYJ
- Type
- protein
- Length
- 918 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Circadian clock protein kinase kaic
- EC
- 2.7.11.1
- UniProt
- Q79PF4
- Ligands
- ATP, MG
- Pockets
- 13 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Circadian clock protein kinase kaic (EC 2.7.11.1) | protein | 458 | 34% helix, 28% strand | Q79PF4 |
| B | Circadian clock protein kinase kaic (EC 2.7.11.1) | protein | 460 | 33% helix, 27% strand | Q79PF4 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 4 copies · chains A, B
- MG · Magnesium ion · metal · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 437 | 0.78 | 0.87 | 64 | ATP, MG |
| 2 | 158 | 0.75 | 0.93 | 31 | ATP, MG |
| 3 | 499 | 0.71 | 0.81 | 72 | empty |
| 4 | 354 | 0.66 | 0.81 | 49 | empty |
| 5 | 165 | 0.66 | 0.86 | 29 | empty |
Interfaces
1 interface between chains.
- A–B · 2521 Ų buried · 34 hydrogen bonds · protein-protein
Compared structures
- 7DYJ · Crystal Structure of Cyanobacterial Circadian Clock Protein KaiC · the same entry in another collection · chain A against A, TM-score 1.00
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 Q79PF4
- Elsewhere: RCSB PDB 7DYJ · PDBe 7DYJ · UniProt Q79PF4
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