Research workbench
Crystal structure of the redox-active cofactor dbmib bound to the full length circadian clock protein kaia from synechococcus elongatus
Analyse Crystal structure of the redox-active cofactor dbmib bound to the full length… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4G86
- Type
- protein
- Length
- 564 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Circadian clock protein kaia
- UniProt
- Q79PF6
- Ligands
- BNT
- Pockets
- 12 · best druggability 0.67
Structure
x-ray diffraction · 1 distinct chain · 52% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Circadian clock protein kaia | protein | 282 | 52% helix, 12% strand | Q79PF6 |
Ligands and binding sites
- BNT · 2,5-dibromo-3-isopropyl-6-methylbenzo-1,4-quinone · ligand · 4 copies · chains A, B
- GOL · Glycerol · additive · 2 copies · chains A, B
- 1PE · Pentaethylene glycol · additive · chains A
- 2PE · Nonaethylene glycol · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 308 | 0.67 | 0.82 | 41 | empty |
| 2 | 314 | 0.65 | 0.81 | 39 | GOL |
| 3 | 244 | 0.55 | 0.77 | 24 | 1PE, 2PE, BNT |
| 4 | 80 | 0.51 | 0.85 | 21 | empty |
| 5 | 127 | 0.51 | 0.81 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 3376 Ų buried · 49 hydrogen bonds · protein-protein
Compared structures
- 4G86 · Crystal structure of the redox-active cofactor DBMIB bound to the full length circadian… · the same entry in another collection · chain A against A, TM-score 1.00
- Q79PF6 · AlphaFold monomer V2.0 prediction for circadian clock protein kaia (Q79PF6) · a predicted model of the same protein · chain A against A, TM-score 0.96
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 Q79PF6
- Elsewhere: RCSB PDB 4G86 · PDBe 4G86 · UniProt Q79PF6
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