Research workbench
Crystal structure of the T3-bound tr-beta ligand-binding domain in complex with rxr-alpha
Analyse Crystal structure of the T3-bound tr-beta ligand-binding domain in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4ZO1
- Type
- protein
- Length
- 449 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thyroid hormone receptor beta; Nuclear receptor coactivator 2; Retinoic acid receptor…
- UniProt
- P10828, P19793
- Ligands
- T3
- Pockets
- 10 · best druggability 0.83
Structure
x-ray diffraction · 3 distinct chains · 65% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| X | Thyroid hormone receptor beta | protein | 242 | 64% helix, 5% strand | P10828 |
| A | Nuclear receptor coactivator 2 | protein | 8 | 50% helix, 0% strand | — |
| B | Retinoic acid receptor rxr-alpha | protein | 199 | 66% helix, 2% strand | P19793 |
Ligands and binding sites
- T3 · 3,5,3'triiodothyronine · ligand · chains X
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 199 | 0.83 | 0.97 | 29 | T3 |
| 2 | 328 | 0.59 | 0.77 | 27 | empty |
| 3 | 65 | 0.55 | 0.88 | 18 | empty |
| 4 | 291 | 0.54 | 0.75 | 41 | empty |
| 5 | 126 | 0.51 | 0.80 | 22 | empty |
Interfaces
2 interfaces between chains.
- X–B · 1021 Ų buried · 7 hydrogen bonds · protein-protein
- X–A · 395 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 4ZO1 · Crystal Structure of the T3-bound TR-beta Ligand-binding Domain in complex with RXR-alpha · the same entry in another collection · chain X against X, TM-score 1.00
- P10828 · AlphaFold monomer V2.0 prediction for thyroid hormone receptor beta (P10828) · a predicted model of the same protein · chain X 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
- Every structure of UniProt P19793
- Elsewhere: RCSB PDB 4ZO1 · PDBe 4ZO1 · UniProt P10828 · UniProt P19793
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