MolNFT v1 · #167361 · protein
Human lrh-1 ligand-binding domain bound to agonist cpd 15 and fragment of coregulator tif-2
6VIF · Nuclear receptor subfamily 5 group a member 2: “Human lrh-1 ligand-binding domain bound to agonist cpd 15 and fragment of coregulator tif-2”. X-ray diffraction, 1 ligand (QY4), 3 pockets (best druggability 0.87). MolNFT v1 #167361…
- PDB
- 6VIF
- Type
- protein
- Length
- 246 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nuclear receptor subfamily 5 group a member 2; Nuclear receptor coactivator 2
- UniProt
- O00482, Q15596
- Ligands
- QY4
- Pockets
- 3 · best druggability 0.87
Structure
x-ray diffraction · 2 distinct chains · 73% helix, 2% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nuclear receptor subfamily 5 group a member 2 | protein | 235 | 73% helix, 3% strand | O00482 |
| B | Nuclear receptor coactivator 2 | protein | 11 | 73% helix, 0% strand | Q15596 |
Ligands and binding sites
- QY4 · N-[(8beta,11alpha,12alpha)-8-{[methyl(phenyl) amino]methyl}-1,6:7,14-dicycloprosta-1(6),2,4,7(14)-tetraen-11-yl]sulfuric diamide · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 441 | 0.87 | 0.93 | 36 | QY4 |
| 2 | 89 | 0.58 | 0.86 | 21 | empty |
| 3 | 64 | 0.35 | 0.77 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 605 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 6VIF · Human LRH-1 ligand-binding domain bound to agonist cpd 15 and fragment of coregulator… · the same entry in another collection · chain A against A, TM-score 1.00
- O00482 · AlphaFold monomer V2.0 prediction for nuclear receptor subfamily 5 group a member 2… · a predicted model of the same protein · chain A 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 O00482
- Every structure of UniProt Q15596
- Elsewhere: RCSB PDB 6VIF · PDBe 6VIF · UniProt O00482 · UniProt Q15596
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