Research workbench
Crystal structure of human NUR77 ligand-binding domain in complex with ethyl 2-[2,3,4 trimethoxy-6(1-OCTANOYL)PHENYL]ACETATE
Analyse Crystal structure of human NUR77 ligand-binding domain in complex with ethyl… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3V3Q
- Type
- protein
- Length
- 476 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
- TMY, NA
- Pockets
- 7 · best druggability 0.58
Structure
x-ray diffraction · 2 distinct chains · 67% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nuclear receptor subfamily 4 group a member 1 | protein | 237 | 67% helix, 4% strand | P22736 |
| B | Nuclear receptor subfamily 4 group a member 1 | protein | 239 | 68% helix, 4% strand | P22736 |
Ligands and binding sites
- TMY · ethyl (2,3,4-trimethoxy-6-octanoylphenyl)acetate · ligand · 2 copies · chains A
- NA · Sodium ion · metal · chains B
- GOL · Glycerol · additive · 4 copies · chains A, B
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 | 141 | 0.58 | 0.83 | 21 | GOL |
| 2 | 231 | 0.53 | 0.77 | 28 | empty |
| 3 | 107 | 0.44 | 0.78 | 17 | GOL |
| 4 | 138 | 0.44 | 0.76 | 16 | empty |
| 5 | 142 | 0.44 | 0.76 | 22 | TMY |
Interfaces
1 interface between chains.
- A–B · 633 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3V3Q · Crystal Structure of Human Nur77 Ligand-binding Domain in Complex with Ethyl 2-[2,3,4… · the same entry in another collection · chain A against A, 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 0.97
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 3V3Q · PDBe 3V3Q · UniProt P22736
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