Research workbench
Structure and kinetics of the lov domain of zeitlupe determine its circadian function in arabidopsis
Analyse Structure and kinetics of the lov domain of zeitlupe determine its circadian… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5SVV
- Type
- protein
- Length
- 493 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Adagio protein 1
- UniProt
- Q94BT6
- Ligands
- FMN
- Pockets
- 5 · best druggability 0.72
Structure
x-ray diffraction · 4 distinct chains · 23% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D | Adagio protein 1 | protein | 120 | 23% helix, 37% strand | Q94BT6 |
| A | Adagio protein 1 | protein | 116 | 25% helix, 34% strand | Q94BT6 |
| B | Adagio protein 1 | protein | 135 | 23% helix, 31% strand | Q94BT6 |
| C | Adagio protein 1 | protein | 122 | 23% helix, 34% strand | Q94BT6 |
Ligands and binding sites
- FMN · Flavin mononucleotide · ligand · 4 copies · chains D, A, B, C
- ACT · Acetate ion · additive · 3 copies · chains A, B, D, C
- GOL · Glycerol · additive · 2 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 182 | 0.72 | 0.89 | 25 | FMN |
| 2 | 167 | 0.71 | 0.89 | 23 | FMN |
| 3 | 187 | 0.69 | 0.87 | 24 | FMN |
| 4 | 170 | 0.69 | 0.88 | 25 | FMN |
| 5 | 68 | 0.34 | 0.76 | 20 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1308 Ų buried · 23 hydrogen bonds · protein-protein
- D–C · 716 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 313 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 5SVV · Structure and kinetics of the LOV domain of ZEITLUPE determine its circadian function in… · the same entry in another collection · chain C against C, TM-score 1.00
- Q94BT6 · AlphaFold monomer V2.0 prediction for adagio protein 1 (Q94BT6) · a predicted model of the same protein · chain D against A, TM-score 0.99
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 Q94BT6
- Elsewhere: RCSB PDB 5SVV · PDBe 5SVV · UniProt Q94BT6
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