Research workbench
Thyroid hormone beta DNA binding domain homodimer with inverted palindrome TRE
Analyse Thyroid hormone beta DNA binding domain homodimer with inverted palindrome TRE in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3M9E
- Type
- protein + DNA
- Length
- 487 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.406
- Source
- Rattus norvegicus; SYNTHETIC CONSTRUCT
- Molecule
- Thyroid hormone receptor beta; DNA (5'-D(*AP*TP*TP*GP*AP*CP*CP*TP*CP*AP*GP*CP*TP*GP*AP*GP*…
- UniProt
- P18113
- Ligands
- ZN
- Pockets
- 10 · best druggability 0.53
Structure
x-ray diffraction · resolution 2.406 · 5 distinct chains · 49% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Thyroid hormone receptor beta | protein | 101 | 49% helix, 4% strand | P18113 |
| B | Thyroid hormone receptor beta | protein | 99 | 49% helix, 6% strand | P18113 |
| C, D, G, H | DNA (5'-D(*AP*TP*TP*GP*AP*CP*CP*TP*CP*AP*GP*CP*TP*GP*AP*GP*GP*TP*CP*AP*AP*T)-3') | dna | 22 | — | — |
| E | Thyroid hormone receptor beta | protein | 102 | 47% helix, 6% strand | P18113 |
| F | Thyroid hormone receptor beta | protein | 97 | 49% helix, 6% strand | P18113 |
Ligands and binding sites
- ZN · Zinc ion · metal · 8 copies · chains A, B, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 312 | 0.53 | 0.75 | 25 | empty |
| 2 | 100 | 0.50 | 0.82 | 13 | empty |
| 3 | 206 | 0.47 | 0.75 | 17 | empty |
| 4 | 122 | 0.39 | 0.75 | 25 | empty |
| 5 | 73 | 0.37 | 0.78 | 12 | empty |
Interfaces
12 interfaces between chains.
- G–H · 971 Ų buried · 97 hydrogen bonds · nucleic-nucleic
- C–D · 966 Ų buried · 94 hydrogen bonds · nucleic-nucleic
- B–C · 640 Ų buried · 15 hydrogen bonds · protein-nucleic
- E–H · 620 Ų buried · 16 hydrogen bonds · protein-nucleic
- A–D · 612 Ų buried · 13 hydrogen bonds · protein-nucleic
Compared structures
- 3M9E · Thyroid hormone beta DNA binding domain homodimer with inverted palindrome tre · the same entry in another collection · chain H against H, TM-score 1.00
- P18113 · AlphaFold monomer V2.0 prediction for thyroid hormone receptor beta (P18113) · a predicted model of the same protein · chain E against A, TM-score 0.98
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 P18113
- Elsewhere: RCSB PDB 3M9E · PDBe 3M9E · UniProt P18113
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