Research workbench
Human nuclear receptor liver receptor homologue-1, lrh-1, bound to phospholipid and a fragment of human shp
Analyse Human nuclear receptor liver receptor homologue-1, lrh-1, bound to phospholipid… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1YUC
- Type
- protein
- Length
- 505 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Orphan nuclear receptor NR5A2; Nuclear receptor 0B2
- UniProt
- O00482, Q15466
- Ligands
- EPH
- Pockets
- 8 · best druggability 0.85
Structure
x-ray diffraction · 4 distinct chains · 70% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Orphan nuclear receptor NR5A2 | protein | 240 | 71% helix, 3% strand | O00482 |
| B | Orphan nuclear receptor NR5A2 | protein | 240 | 70% helix, 3% strand | O00482 |
| C | Nuclear receptor 0B2 | protein | 14 | 57% helix, 0% strand | Q15466 |
| D | Nuclear receptor 0B2 | protein | 11 | 73% helix, 0% strand | Q15466 |
Ligands and binding sites
- EPH · L-alpha-phosphatidyl-beta-oleoyl-gamma-palmitoyl-phosphatidylethanolamine · ligand · 2 copies · chains A, B
- GOL · Glycerol · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 665 | 0.85 | 0.88 | 50 | EPH |
| 2 | 729 | 0.83 | 0.87 | 65 | EPH |
| 3 | 143 | 0.75 | 0.93 | 29 | empty |
| 4 | 142 | 0.74 | 0.92 | 25 | empty |
| 5 | 94 | 0.70 | 0.93 | 21 | empty |
Interfaces
3 interfaces between chains.
- A–B · 925 Ų buried · 23 hydrogen bonds · protein-protein
- A–C · 596 Ų buried · 6 hydrogen bonds · protein-protein
- B–D · 535 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 1YUC · Human Nuclear Receptor Liver Receptor Homologue-1, LRH-1, Bound to Phospholipid and a… · the same entry in another collection · chain D against D, 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 B against A, TM-score 0.98
- Q15466 · AlphaFold monomer V2.0 prediction for nuclear receptor subfamily 0 group B member 2… · a predicted model of the same protein · chain D against A, TM-score 0.73
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 Q15466
- Elsewhere: RCSB PDB 1YUC · PDBe 1YUC · UniProt O00482 · UniProt Q15466
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