Research workbench
Crystal structure of TR3 lbd in complex with molecule 3
Analyse Crystal structure of TR3 lbd in complex with molecule 3 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4WHG
- Type
- protein
- Length
- 466 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nuclear receptor subfamily 4 group a member 1
- UniProt
- P22736
- Ligands
- 3NB
- Pockets
- 8 · best druggability 0.58
Structure
x-ray diffraction · 2 distinct chains · 69% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Nuclear receptor subfamily 4 group a member 1 | protein | 232 | 69% helix, 4% strand | P22736 |
| A | Nuclear receptor subfamily 4 group a member 1 | protein | 234 | 69% helix, 4% strand | P22736 |
Ligands and binding sites
- 3NB · 1-(3,4,5-trihydroxyphenyl)octan-1-one · ligand · chains A
- GOL · Glycerol · additive · 5 copies · chains B, A
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 | 124 | 0.58 | 0.84 | 21 | 3NB |
| 2 | 227 | 0.52 | 0.76 | 26 | empty |
| 3 | 168 | 0.47 | 0.76 | 17 | empty |
| 4 | 120 | 0.43 | 0.77 | 18 | empty |
| 5 | 113 | 0.41 | 0.76 | 16 | GOL |
Interfaces
1 interface between chains.
- B–A · 631 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (additive adduct).
Compared structures
- 4WHG · Crystal Structure of TR3 LBD in complex with Molecule 3 · the same entry in another collection · chain B against B, TM-score 1.00
- P22736 · AlphaFold monomer V2.0 prediction for nuclear receptor subfamily 4 group a member 1… · 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 P22736
- Elsewhere: RCSB PDB 4WHG · PDBe 4WHG · UniProt P22736
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