MolNFT v1 · #61774 · protein
Crystal structure of full length circadian clock protein kaic with correct geometry at phosphorylation sites
3DVL · Circadian clock protein kinase kaic: “Crystal structure of full length circadian clock protein kaic with correct geometry at phosphorylation sites”. X-ray diffraction, 2 ligands (ATP, MG), 20 pockets (best druggability 0.83). MolNFT…
- PDB
- 3DVL
- 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 · 31% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, F | Circadian clock protein kinase kaic (EC 2.7.11.1) | protein | 506 | 30% helix, 25% strand | Q79PF4 |
| B | Circadian clock protein kinase kaic (EC 2.7.11.1) | protein | 491 | 31% helix, 26% strand | Q79PF4 |
| C | Circadian clock protein kinase kaic (EC 2.7.11.1) | protein | 488 | 30% helix, 26% strand | Q79PF4 |
| D | Circadian clock protein kinase kaic (EC 2.7.11.1) | protein | 485 | 31% helix, 26% strand | Q79PF4 |
| E | Circadian clock protein kinase kaic (EC 2.7.11.1) | protein | 492 | 32% helix, 25% strand | Q79PF4 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 12 copies · chains A, B, C, D, E, F
- MG · Magnesium ion · metal · 6 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 | 970 | 0.83 | 0.84 | 106 | ATP |
| 2 | 628 | 0.80 | 0.85 | 77 | empty |
| 3 | 592 | 0.79 | 0.84 | 85 | empty |
| 4 | 665 | 0.78 | 0.84 | 78 | ATP |
| 5 | 654 | 0.78 | 0.84 | 74 | ATP |
Interfaces
6 interfaces between chains.
- A–B · 3623 Ų buried · 58 hydrogen bonds · protein-protein
- A–F · 3552 Ų buried · 55 hydrogen bonds · protein-protein
- C–D · 3513 Ų buried · 58 hydrogen bonds · protein-protein
- D–E · 3501 Ų buried · 50 hydrogen bonds · protein-protein
- B–C · 3483 Ų buried · 57 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 modified (phosphorylation).
Compared structures
- 3DVL · Crystal Structure of Full Length Circadian Clock Protein KaiC with Correct Geometry at… · 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 3DVL · PDBe 3DVL · UniProt Q79PF4
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