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
- 4TL9
- Type
- protein
- Length
- 1,312 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
- AGS, MG, CL
- Pockets
- 19 · best druggability 0.81
Structure
x-ray diffraction · 5 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 | 220 | 34% helix, 29% strand | Q79PF4 |
| B, E | Circadian clock protein kinase kaic (EC 2.7.11.1) | protein | 218 | 34% helix, 29% strand | Q79PF4 |
| C | Circadian clock protein kinase kaic (EC 2.7.11.1) | protein | 222 | 33% helix, 29% strand | Q79PF4 |
| D | Circadian clock protein kinase kaic (EC 2.7.11.1) | protein | 220 | 34% helix, 29% strand | Q79PF4 |
| F | Circadian clock protein kinase kaic (EC 2.7.11.1) | protein | 214 | 33% helix, 30% strand | Q79PF4 |
Ligands and binding sites
- AGS · Phosphothiophosphoric 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, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 852 | 0.81 | 0.84 | 79 | MG, AGS |
| 2 | 912 | 0.81 | 0.83 | 78 | MG, AGS |
| 3 | 423 | 0.80 | 0.88 | 67 | MG, CL, AGS |
| 4 | 269 | 0.80 | 0.92 | 39 | MG, AGS |
| 5 | 277 | 0.78 | 0.91 | 39 | MG, AGS |
Interfaces
6 interfaces between chains.
- A–F · 1352 Ų buried · 27 hydrogen bonds · protein-protein
- B–C · 1313 Ų buried · 24 hydrogen bonds · protein-protein
- C–D · 1295 Ų buried · 21 hydrogen bonds · protein-protein
- A–B · 1278 Ų buried · 27 hydrogen bonds · protein-protein
- E–F · 1179 Ų buried · 24 hydrogen bonds · protein-protein
Compared structures
- 4TL9 · 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 4TL9 · PDBe 4TL9 · UniProt Q79PF4
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