Research workbench
Small molecule agonists and antagonists of F-box protein-substrate interactions in auxin perception and signaling
Analyse Small molecule agonists and antagonists of F-box protein-substrate interactions… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3C6N
- Type
- protein
- Length
- 624 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- SKP1-like protein 1A; Transport inhibitor response 1
- UniProt
- Q39255, Q570C0
- Ligands
- IHP, 2S8
- Pockets
- 4 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | SKP1-like protein 1A | protein | 57 | 58% helix, 0% strand | Q39255 |
| B | Transport inhibitor response 1 | protein | 567 | 36% helix, 18% strand | Q570C0 |
Ligands and binding sites
- IHP · Inositol hexakisphosphate · ligand · chains B
- 2S8 · (2S)-8-[(tert-butoxycarbonyl)amino]-2-(1H-indol-3-yl)octanoic acid · ligand · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 828 | 0.73 | 0.78 | 98 | IHP, 2S8 |
| 2 | 78 | 0.37 | 0.77 | 15 | empty |
| 3 | 71 | 0.32 | 0.75 | 20 | empty |
| 4 | 66 | 0.30 | 0.75 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 1544 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
- 3C6N · Small molecule agonists and antagonists of F-box protein-substrate interactions in auxin… · the same entry in another collection · chain A against A, TM-score 1.00
- Q570C0 · AlphaFold monomer V2.0 prediction for protein transport inhibitor response 1 (Q570C0) · a predicted model of the same protein · chain B against A, TM-score 0.99
- Q39255 · AlphaFold monomer V2.0 prediction for SKP1-like protein 1A (Q39255) · a predicted model of the same protein · chain A against A, TM-score 0.86
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 Q39255
- Every structure of UniProt Q570C0
- Elsewhere: RCSB PDB 3C6N · PDBe 3C6N · UniProt Q39255 · UniProt Q570C0
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