Research workbench
Crystal structure of human tr beta ligand-binding domain complexed with a potent subtype-selective thyromimetic
Analyse Crystal structure of human tr beta ligand-binding domain complexed with a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1N46
- Type
- protein
- Length
- 487 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thyroid hormone receptor beta-1
- UniProt
- P10828
- Ligands
- PFA
- Pockets
- 7 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 66% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Thyroid hormone receptor beta-1 | protein | 248 | 64% helix, 4% strand | P10828 |
| B | Thyroid hormone receptor beta-1 | protein | 239 | 67% helix, 4% strand | P10828 |
Ligands and binding sites
- PFA · [4-(4-hydroxy-3-isopropyl-phenoxy)-3,5-dimethyl-phenyl]-6-azauracil · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 162 | 0.84 | 0.98 | 26 | PFA |
| 2 | 154 | 0.82 | 0.98 | 27 | PFA |
| 3 | 1146 | 0.81 | 0.82 | 82 | empty |
| 4 | 87 | 0.39 | 0.77 | 19 | empty |
| 5 | 86 | 0.36 | 0.76 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 657 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 1N46 · Crystal structure of human tr beta ligand-binding domain complexed with a potent… · the same entry in another collection · chain A against A, TM-score 1.00
- P10828 · AlphaFold monomer V2.0 prediction for thyroid hormone receptor beta (P10828) · a predicted model of the same protein · chain B 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 P10828
- Elsewhere: RCSB PDB 1N46 · PDBe 1N46 · UniProt P10828
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