MolNFT v1 · #134144 · protein
Structure and kinetics of the lov domain of zeitlupe determine its circadian function in arabidopsis
5SVG · Adagio protein 1: “Structure and kinetics of the lov domain of zeitlupe determine its circadian function in arabidopsis”. X-ray diffraction, 1 ligand (FMN), 9 pockets (best druggability 0.73). MolNFT v1 #134144 on GenesisL1: 3D…
- PDB
- 5SVG
- Type
- protein
- Length
- 499 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Adagio protein 1
- UniProt
- Q94BT6
- Ligands
- FMN
- Pockets
- 9 · best druggability 0.73
Structure
x-ray diffraction · 3 distinct chains · 24% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Adagio protein 1 | protein | 134 | 24% helix, 30% strand | Q94BT6 |
| A | Adagio protein 1 | protein | 123 | 24% helix, 33% strand | Q94BT6 |
| C, D | Adagio protein 1 | protein | 121 | 23% helix, 34% strand | Q94BT6 |
Ligands and binding sites
- FMN · Flavin mononucleotide · ligand · 4 copies · chains B, A, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 195 | 0.73 | 0.89 | 26 | FMN |
| 2 | 203 | 0.73 | 0.89 | 26 | FMN |
| 3 | 205 | 0.70 | 0.87 | 29 | FMN |
| 4 | 176 | 0.70 | 0.88 | 26 | FMN |
| 5 | 59 | 0.44 | 0.82 | 18 | empty |
Interfaces
3 interfaces between chains.
- B–A · 1340 Ų buried · 21 hydrogen bonds · protein-protein
- C–D · 765 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 565 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 5SVG · Structure and kinetics of the LOV domain of ZEITLUPE determine its circadian function in… · the same entry in another collection · chain D against D, 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 0.98
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 5SVG · PDBe 5SVG · UniProt Q94BT6
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