MolNFT v1 · #101743 · protein
Crystal structure of T. elongatus bp-1 clock protein kaic
4O0M · Circadian clock protein kinase kaic: “Crystal structure of T. elongatus bp-1 clock protein kaic”. X-ray diffraction, 2 ligands (ATP, MG), 20 pockets (best druggability 0.83). MolNFT v1 #101743 on GenesisL1: 3D structure, binding…
- PDB
- 4O0M
- Type
- protein
- Length
- 1,474 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Circadian clock protein kinase kaic
- EC
- 2.7.11.1
- UniProt
- Q79V60
- Ligands
- ATP, MG
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 3 distinct chains · 29% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Circadian clock protein kinase kaic (EC 2.7.11.1) | protein | 494 | 29% helix, 26% strand | Q79V60 |
| B | Circadian clock protein kinase kaic (EC 2.7.11.1) | protein | 490 | 29% helix, 26% strand | Q79V60 |
| C | Circadian clock protein kinase kaic (EC 2.7.11.1) | protein | 490 | 29% helix, 26% strand | Q79V60 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 6 copies · chains A, B, C
- MG · Magnesium ion · metal · 6 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 987 | 0.83 | 0.84 | 120 | MG, ATP |
| 2 | 632 | 0.78 | 0.84 | 73 | ATP |
| 3 | 438 | 0.75 | 0.84 | 74 | empty |
| 4 | 194 | 0.73 | 0.90 | 31 | MG, ATP |
| 5 | 171 | 0.72 | 0.90 | 28 | MG, ATP |
Interfaces
2 interfaces between chains.
- B–C · 3621 Ų buried · 46 hydrogen bonds · protein-protein
- A–B · 3488 Ų buried · 44 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 modified (phosphorylation).
Compared structures
- 4O0M · Crystal structure of T. Elongatus BP-1 Clock Protein KaiC · the same entry in another collection · chain A against A, TM-score 1.00
- Q79V60 · AlphaFold monomer V2.0 prediction for circadian clock protein kinase kaic (Q79V60) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 Q79V60
- Elsewhere: RCSB PDB 4O0M · PDBe 4O0M · UniProt Q79V60
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