Research workbench
Crystal structure of the phosphorylation-site mutant S431D of the kaic circadian clock protein
Analyse Crystal structure of the phosphorylation-site mutant S431D of the kaic… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3K09
- Type
- protein
- Length
- 2,968 residues
- Chains
- 6
- 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
- 20 · best druggability 0.83
Structure
x-ray diffraction · 5 distinct chains · 30% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, F | Circadian clock protein kinase kaic (EC 2.7.11.1) | protein | 506 | 29% helix, 23% strand | Q79PF4 |
| B | Circadian clock protein kinase kaic (EC 2.7.11.1) | protein | 491 | 31% helix, 24% strand | Q79PF4 |
| C | Circadian clock protein kinase kaic (EC 2.7.11.1) | protein | 488 | 28% helix, 24% strand | Q79PF4 |
| D | Circadian clock protein kinase kaic (EC 2.7.11.1) | protein | 485 | 30% helix, 24% strand | Q79PF4 |
| E | Circadian clock protein kinase kaic (EC 2.7.11.1) | protein | 492 | 30% helix, 22% strand | Q79PF4 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 12 copies · chains A, B, C, D, E, F
- MG · Magnesium ion · metal · 20 copies · chains A, B, F, C, D, E
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 | 944 | 0.83 | 0.84 | 102 | MG, ATP |
| 2 | 949 | 0.82 | 0.84 | 105 | MG, ATP |
| 3 | 285 | 0.81 | 0.93 | 39 | MG, ATP |
| 4 | 244 | 0.81 | 0.94 | 37 | MG, ATP |
| 5 | 239 | 0.80 | 0.93 | 38 | MG, ATP |
Interfaces
6 interfaces between chains.
- A–B · 3646 Ų buried · 49 hydrogen bonds · protein-protein
- A–F · 3631 Ų buried · 47 hydrogen bonds · protein-protein
- C–D · 3503 Ų buried · 50 hydrogen bonds · protein-protein
- B–C · 3495 Ų buried · 52 hydrogen bonds · protein-protein
- D–E · 3488 Ų buried · 47 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 modified (phosphorylation).
Compared structures
- 3K09 · Crystal structure of the phosphorylation-site mutant S431D of the KaiC circadian clock… · 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 3K09 · PDBe 3K09 · UniProt Q79PF4
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