Research workbench
Crystal structure of TR3 lbd in complex with molecule 5
Analyse Crystal structure of TR3 lbd in complex with molecule 5 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4RE8
- Type
- protein
- Length
- 460 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
- 3MJ
- Pockets
- 7 · best druggability 0.60
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 | 227 | 68% helix, 4% strand | P22736 |
| A | Nuclear receptor subfamily 4 group a member 1 | protein | 233 | 69% helix, 4% strand | P22736 |
Ligands and binding sites
- 3MJ · 1-(3,4,5-trihydroxyphenyl)dodecan-1-one · ligand · chains A
- GOL · Glycerol · additive · 4 copies · chains B, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 137 | 0.60 | 0.84 | 21 | 3MJ |
| 2 | 237 | 0.53 | 0.76 | 28 | empty |
| 3 | 171 | 0.46 | 0.75 | 20 | empty |
| 4 | 94 | 0.42 | 0.78 | 20 | empty |
| 5 | 115 | 0.42 | 0.76 | 16 | GOL |
Interfaces
1 interface between chains.
- B–A · 578 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4RE8 · Crystal Structure of TR3 LBD in complex with Molecule 5 · 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 4RE8 · PDBe 4RE8 · UniProt P22736
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