Research workbench
Crystal structure of N-terminal C1 domain of kaic
Analyse Crystal structure of N-terminal C1 domain of kaic in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5YZ8
- Type
- protein
- Length
- 1,324 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
- ANP, MG, CL
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 6 distinct chains · 34% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Circadian clock protein kinase kaic (EC 2.7.11.1) | protein | 222 | 35% helix, 29% strand | Q79PF4 |
| B | Circadian clock protein kinase kaic (EC 2.7.11.1) | protein | 223 | 34% helix, 29% strand | Q79PF4 |
| C | Circadian clock protein kinase kaic (EC 2.7.11.1) | protein | 224 | 35% helix, 29% strand | Q79PF4 |
| D | Circadian clock protein kinase kaic (EC 2.7.11.1) | protein | 216 | 34% helix, 30% strand | Q79PF4 |
| E | Circadian clock protein kinase kaic (EC 2.7.11.1) | protein | 220 | 35% helix, 30% strand | Q79PF4 |
| F | Circadian clock protein kinase kaic (EC 2.7.11.1) | protein | 219 | 34% helix, 28% strand | Q79PF4 |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 6 copies · chains A, B, C, D, E, F
- MG · Magnesium ion · metal · 6 copies · chains A, B, C, D, E, F
- CL · Chloride ion · ion · 6 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, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 323 | 0.81 | 0.91 | 46 | ANP, MG, CL |
| 2 | 299 | 0.80 | 0.91 | 41 | ANP, MG |
| 3 | 344 | 0.79 | 0.89 | 46 | ANP, MG, CL |
| 4 | 269 | 0.79 | 0.91 | 37 | ANP, MG |
| 5 | 308 | 0.79 | 0.90 | 48 | ANP, MG, CL |
Interfaces
6 interfaces between chains.
- A–B · 1096 Ų buried · 12 hydrogen bonds · protein-protein
- C–D · 1079 Ų buried · 20 hydrogen bonds · protein-protein
- E–F · 1068 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 1062 Ų buried · 14 hydrogen bonds · protein-protein
- D–E · 1032 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 5YZ8 · Crystal Structure of N-terminal C1 domain of 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 5YZ8 · PDBe 5YZ8 · UniProt Q79PF4
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