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
- 4TL8
- Type
- protein
- Length
- 1,297 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
- 20 · best druggability 0.83
Structure
x-ray diffraction · 6 distinct chains · 34% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Circadian clock protein kinase kaic (EC 2.7.11.1) | protein | 215 | 34% helix, 30% strand | Q79PF4 |
| B | Circadian clock protein kinase kaic (EC 2.7.11.1) | protein | 215 | 34% helix, 30% strand | Q79PF4 |
| C | Circadian clock protein kinase kaic (EC 2.7.11.1) | protein | 221 | 33% helix, 29% strand | Q79PF4 |
| D | Circadian clock protein kinase kaic (EC 2.7.11.1) | protein | 217 | 34% helix, 29% strand | Q79PF4 |
| E | Circadian clock protein kinase kaic (EC 2.7.11.1) | protein | 216 | 34% helix, 30% strand | Q79PF4 |
| F | Circadian clock protein kinase kaic (EC 2.7.11.1) | protein | 213 | 34% helix, 31% 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
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 980 | 0.83 | 0.84 | 97 | MG, CL, AGS |
| 2 | 277 | 0.80 | 0.92 | 39 | MG, AGS |
| 3 | 309 | 0.79 | 0.90 | 44 | AGS, MG |
| 4 | 267 | 0.79 | 0.91 | 37 | MG, AGS |
| 5 | 694 | 0.79 | 0.83 | 61 | MG, AGS |
Interfaces
6 interfaces between chains.
- B–C · 1295 Ų buried · 25 hydrogen bonds · protein-protein
- A–F · 1280 Ų buried · 28 hydrogen bonds · protein-protein
- C–D · 1252 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 1183 Ų buried · 24 hydrogen bonds · protein-protein
- D–E · 1183 Ų buried · 25 hydrogen bonds · protein-protein
Compared structures
- 4TL8 · 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 4TL8 · PDBe 4TL8 · UniProt Q79PF4
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