Research workbench
Crystal structure of cyanobacterial circadian clock protein kaic
Analyse Crystal structure of cyanobacterial circadian clock protein kaic in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7DY2
- Type
- protein
- Length
- 5,548 residues
- Chains
- 12
- 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, ADP, MG
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 12 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 | 464 | 30% helix, 28% strand | Q79PF4 |
| B | Circadian clock protein kinase kaic (EC 2.7.11.1) | protein | 461 | 29% helix, 25% strand | Q79PF4 |
| E | Circadian clock protein kinase kaic (EC 2.7.11.1) | protein | 464 | 28% helix, 29% strand | Q79PF4 |
| F | Circadian clock protein kinase kaic (EC 2.7.11.1) | protein | 467 | 32% helix, 24% strand | Q79PF4 |
| C | Circadian clock protein kinase kaic (EC 2.7.11.1) | protein | 462 | 28% helix, 25% strand | Q79PF4 |
| D | Circadian clock protein kinase kaic (EC 2.7.11.1) | protein | 458 | 28% helix, 27% strand | Q79PF4 |
| G | Circadian clock protein kinase kaic (EC 2.7.11.1) | protein | 459 | 27% helix, 24% strand | Q79PF4 |
| H | Circadian clock protein kinase kaic (EC 2.7.11.1) | protein | 460 | 31% helix, 25% strand | Q79PF4 |
| K | Circadian clock protein kinase kaic (EC 2.7.11.1) | protein | 465 | 30% helix, 28% strand | Q79PF4 |
| L | Circadian clock protein kinase kaic (EC 2.7.11.1) | protein | 457 | 27% helix, 24% strand | Q79PF4 |
| I | Circadian clock protein kinase kaic (EC 2.7.11.1) | protein | 467 | 30% helix, 27% strand | Q79PF4 |
| J | Circadian clock protein kinase kaic (EC 2.7.11.1) | protein | 464 | 30% helix, 28% strand | Q79PF4 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 13 copies · chains A, B, C, E, F, D, G, H, I, K, L, J
- ADP · Adenosine-5'-diphosphate · ligand · 11 copies · chains A, B, F, C, D, E, G, H, I, K, L, J
- MG · Magnesium ion · metal · 12 copies · chains A, B, C, E, F, D, G, H, I, K, L, J
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 | 1011 | 0.85 | 0.86 | 122 | ADP |
| 2 | 1101 | 0.85 | 0.86 | 128 | ADP |
| 3 | 1060 | 0.85 | 0.86 | 121 | ATP |
| 4 | 974 | 0.84 | 0.85 | 115 | ADP |
| 5 | 559 | 0.84 | 0.89 | 71 | ATP |
Interfaces
14 interfaces between chains.
- A–F · 2804 Ų buried · 32 hydrogen bonds · protein-protein
- I–J · 2777 Ų buried · 34 hydrogen bonds · protein-protein
- H–I · 2753 Ų buried · 22 hydrogen bonds · protein-protein
- A–B · 2731 Ų buried · 38 hydrogen bonds · protein-protein
- E–F · 2721 Ų buried · 34 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 11 modified (phosphorylation).
Compared structures
- 7DY2 · Crystal Structure of Cyanobacterial Circadian Clock Protein 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 7DY2 · PDBe 7DY2 · UniProt Q79PF4
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