MolNFT v1 · #134159 · protein
Structure and kinetics of the lov domain of zeitlupe determine its circadian function in arabidopsis
5SVV · Adagio protein 1: “Structure and kinetics of the lov domain of zeitlupe determine its circadian function in arabidopsis”. X-ray diffraction, 1 ligand (FMN), 5 pockets (best druggability 0.72). MolNFT v1 #134159 on GenesisL1: 3D…
- 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
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.