Research workbench
Crystal structure of full length circadian clock protein kaic with correct geometry at phosphorylation sites
Analyse Crystal structure of full length circadian clock protein kaic with correct… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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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