Research workbench
Crystal structure of human lrh-1 bound with tif-2 peptide and phosphatidylglycerol
Analyse Crystal structure of human lrh-1 bound with tif-2 peptide and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1YOK
- Type
- protein
- Length
- 261 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Orphan nuclear receptor NR5A2; Nuclear receptor coactivator 2
- UniProt
- O00482, Q15596
- Ligands
- P6L
- Pockets
- 5 · best druggability 0.83
Structure
x-ray diffraction · 3 distinct chains · 69% helix, 2% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Orphan nuclear receptor NR5A2 | protein | 236 | 69% helix, 3% strand | O00482 |
| B | Nuclear receptor coactivator 2 | protein | 11 | 73% helix, 0% strand | Q15596 |
| C | Nuclear receptor coactivator 2 | protein | 14 | 57% helix, 0% strand | Q15596 |
Ligands and binding sites
- P6L · (2S)-3-{[{[(2S)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-2-[(6E)-hexadec-6-enoyloxy]propyl (8E)-octadec-8-enoate · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 666 | 0.83 | 0.87 | 56 | P6L |
| 2 | 104 | 0.64 | 0.89 | 20 | empty |
| 3 | 72 | 0.30 | 0.73 | 14 | empty |
| 4 | 69 | 0.29 | 0.74 | 16 | empty |
| 5 | 62 | 0.29 | 0.74 | 13 | empty |
Interfaces
3 interfaces between chains.
- A–B · 608 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 278 Ų buried · 0 hydrogen bonds · protein-protein
- A–C · 112 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 1YOK · crystal structure of human LRH-1 bound with TIF-2 peptide and phosphatidylglycerol · 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 1YOK · PDBe 1YOK · UniProt O00482 · UniProt Q15596
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