MolNFT v1 · #187233 · protein
Compressed conformation of nighttime state kaic
7S65 · Circadian clock protein kinase kaic: “Compressed conformation of nighttime state kaic”. Electron microscopy, 3 ligands (ATP, ADP, MG), 20 pockets (best druggability 0.85). MolNFT v1 #187233 on GenesisL1: 3D structure, binding sites…
- PDB
- 7S65
- Type
- protein
- Length
- 2,760 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Circadian clock protein kinase kaic
- EC
- 2.7.11.1
- UniProt
- Q79PF4
- Ligands
- ATP, ADP, MG
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · 3 distinct chains · 33% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Circadian clock protein kinase kaic (EC 2.7.11.1) | protein | 456 | 33% helix, 24% strand | Q79PF4 |
| B, E | Circadian clock protein kinase kaic (EC 2.7.11.1) | protein | 461 | 34% helix, 27% strand | Q79PF4 |
| C, F | Circadian clock protein kinase kaic (EC 2.7.11.1) | protein | 463 | 30% helix, 27% strand | Q79PF4 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 10 copies · chains A, B, C, D, E, F
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, B, D, E
- MG · Magnesium ion · metal · 12 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 849 | 0.85 | 0.87 | 111 | empty |
| 2 | 889 | 0.83 | 0.85 | 106 | empty |
| 3 | 262 | 0.80 | 0.93 | 36 | ATP, MG |
| 4 | 272 | 0.80 | 0.92 | 41 | ATP, MG |
| 5 | 654 | 0.78 | 0.84 | 74 | ATP, MG |
Interfaces
6 interfaces between chains.
- E–F · 2975 Ų buried · 38 hydrogen bonds · protein-protein
- B–C · 2960 Ų buried · 38 hydrogen bonds · protein-protein
- C–D · 2937 Ų buried · 29 hydrogen bonds · protein-protein
- A–F · 2909 Ų buried · 29 hydrogen bonds · protein-protein
- D–E · 2874 Ų buried · 42 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 7S65 · Compressed conformation of nighttime state 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 7S65 · PDBe 7S65 · UniProt Q79PF4
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.