Research workbench
Crystal structure of N-terminal domain of kaic
Analyse Crystal structure of N-terminal 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
- 4TL6
- Type
- protein
- Length
- 667 residues
- Chains
- 3
- 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
- 7 · best druggability 0.82
Structure
x-ray diffraction · 3 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 | 33% helix, 29% strand | Q79PF4 |
| B | Circadian clock protein kinase kaic (EC 2.7.11.1) | protein | 224 | 34% helix, 29% strand | Q79PF4 |
| C | Circadian clock protein kinase kaic (EC 2.7.11.1) | protein | 221 | 33% helix, 29% strand | Q79PF4 |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 3 copies · chains A, B, C
- MG · Magnesium ion · metal · 3 copies · chains A, B, C
- CL · Chloride ion · ion · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 858 | 0.82 | 0.84 | 73 | ANP, MG |
| 2 | 379 | 0.81 | 0.90 | 58 | ANP, MG, CL |
| 3 | 235 | 0.59 | 0.79 | 21 | empty |
| 4 | 114 | 0.51 | 0.81 | 21 | empty |
| 5 | 114 | 0.50 | 0.81 | 22 | empty |
Interfaces
2 interfaces between chains.
- B–C · 1347 Ų buried · 31 hydrogen bonds · protein-protein
- A–B · 1215 Ų buried · 21 hydrogen bonds · protein-protein
Compared structures
- 4TL6 · Crystal structure of N-terminal domain of KaiC · the same entry in another collection · chain B against B, 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 4TL6 · PDBe 4TL6 · UniProt Q79PF4
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