Research workbench
Human liver receptor homologue-1 (lrh-1) bound to a RJW100 stereoisomer and a fragment of tif-2
Analyse Human liver receptor homologue-1 (lrh-1) bound to a RJW100 stereoisomer and a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5SYZ
- 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
- 71W
- Pockets
- 4 · best druggability 0.85
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 | 237 | 73% helix, 3% strand | O00482 |
| C | Nuclear receptor coactivator 2 | protein | 11 | 73% helix, 0% strand | Q15596 |
Ligands and binding sites
- 71W · (1s,3ar,6ar)-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 | 379 | 0.85 | 0.93 | 33 | 71W |
| 2 | 115 | 0.58 | 0.84 | 21 | empty |
| 3 | 52 | 0.33 | 0.78 | 13 | empty |
| 4 | 52 | 0.32 | 0.78 | 14 | empty |
Interfaces
1 interface between chains.
- A–C · 579 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 5SYZ · Human Liver Receptor Homologue-1 (LRH-1) Bound to a RJW100 stereoisomer and a Fragment of… · 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 5SYZ · PDBe 5SYZ · UniProt O00482 · UniProt Q15596
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