MolNFT v1 · #108763 · protein
Crystal structure of TR3 lbd in complex with 1-(3,4,5- TRIHYDROXYPHENYL)DECAN-1-one
4WHF · Nuclear receptor subfamily 4 group a member 1: “Crystal structure of TR3 lbd in complex with 1-(3,4,5- TRIHYDROXYPHENYL)DECAN-1-one”. X-ray diffraction, 1 ligand (3MX), 6 pockets (best druggability 0.62). MolNFT v1 #108763 on…
- PDB
- 4WHF
- 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
- 3MX
- Pockets
- 6 · best druggability 0.62
Structure
x-ray diffraction · 2 distinct chains · 70% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Nuclear receptor subfamily 4 group a member 1 | protein | 229 | 70% helix, 4% strand | P22736 |
| A | Nuclear receptor subfamily 4 group a member 1 | protein | 231 | 69% helix, 4% strand | P22736 |
Ligands and binding sites
- 3MX · 1-(3,4,5-trihydroxyphenyl)decan-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
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 323 | 0.62 | 0.78 | 39 | 3MX, GOL |
| 2 | 257 | 0.52 | 0.75 | 29 | empty |
| 3 | 139 | 0.44 | 0.76 | 18 | empty |
| 4 | 109 | 0.43 | 0.77 | 15 | GOL |
| 5 | 105 | 0.40 | 0.76 | 15 | GOL |
Interfaces
1 interface between chains.
- B–A · 587 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4WHF · Crystal Structure of TR3 LBD in complex with 1-(3,4,5-trihydroxyphenyl)decan-1-one · 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 4WHF · PDBe 4WHF · UniProt P22736
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