Research workbench
Mechanism of auxin perception by the TIR1 ubiqutin ligase
Analyse Mechanism of auxin perception by the TIR1 ubiqutin ligase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2P1N
- Type
- protein
- Length
- 1,421 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- SKP1-like protein 1A; Transport inhibitor response 1 protein; Auxin-responsive protein…
- UniProt
- Q39255, Q570C0, Q38825
- Ligands
- IHP, CFA
- Pockets
- 8 · best druggability 0.79
Structure
x-ray diffraction · 4 distinct chains · 43% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | SKP1-like protein 1A | protein | 126 | 57% helix, 8% strand | Q39255 |
| B, E | Transport inhibitor response 1 protein | protein | 571 | 37% helix, 19% strand | Q570C0 |
| C, F | Auxin-responsive protein IAA7 | protein | 13 | 0% helix, 15% strand | Q38825 |
| D | SKP1-like protein 1A | protein | 127 | 59% helix, 8% strand | Q39255 |
Ligands and binding sites
- IHP · Inositol hexakisphosphate · ligand · 2 copies · chains B, E
- CFA · (2,4-dichlorophenoxy)acetic acid · ligand · 2 copies · chains B, C, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 926 | 0.79 | 0.82 | 94 | IHP, CFA |
| 2 | 1194 | 0.76 | 0.79 | 101 | IHP, CFA |
| 3 | 208 | 0.45 | 0.74 | 39 | empty |
| 4 | 115 | 0.44 | 0.78 | 23 | empty |
| 5 | 90 | 0.41 | 0.78 | 15 | empty |
Interfaces
5 interfaces between chains.
- D–E · 1719 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 1714 Ų buried · 18 hydrogen bonds · protein-protein
- B–C · 710 Ų buried · 6 hydrogen bonds · protein-protein
- E–F · 698 Ų buried · 8 hydrogen bonds · protein-protein
- B–E · 676 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 2P1N · Mechanism of Auxin Perception by the TIR1 Ubiqutin Ligase · the same entry in another collection · chain F against F, 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 0.92
- Q38825 · AlphaFold monomer V2.0 prediction for auxin-responsive protein IAA7 (Q38825) · a predicted model of the same protein · chain C against A, TM-score 0.28
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
- Every structure of UniProt Q38825
- Elsewhere: RCSB PDB 2P1N · PDBe 2P1N · UniProt Q39255 · UniProt Q570C0 · UniProt Q38825
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