MolNFT v1 · #167147 · protein
Lrh-1 bound to ss-RJW100 and a fragment of the TIF2 coactivator
6VC2 · Nuclear receptor subfamily 5 group a member 2: “Lrh-1 bound to ss-RJW100 and a fragment of the TIF2 coactivator”. X-ray diffraction, 1 ligand (QU7), 4 pockets (best druggability 0.86). MolNFT v1 #167147 on GenesisL1: 3D structure…
- PDB
- 6VC2
- Type
- protein
- Length
- 248 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
- QU7
- Pockets
- 4 · best druggability 0.86
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 | 236 | 74% helix, 3% strand | O00482 |
| C | Nuclear receptor coactivator 2 | protein | 12 | 67% helix, 0% strand | Q15596 |
Ligands and binding sites
- QU7 · (1s,3as,6as)-5-hexyl-4-phenyl-3A-(1-phenylethenyl)-1,2, 3,3A,6,6A-hexahydropentalen-1-ol · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 397 | 0.86 | 0.94 | 35 | QU7 |
| 2 | 120 | 0.58 | 0.84 | 21 | empty |
| 3 | 88 | 0.37 | 0.76 | 16 | empty |
| 4 | 54 | 0.31 | 0.76 | 11 | empty |
Interfaces
1 interface between chains.
- A–C · 602 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 6VC2 · LRH-1 bound to SS-RJW100 and a fragment of the Tif2 Coactivator · 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 6VC2 · PDBe 6VC2 · UniProt O00482 · UniProt Q15596
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