Research workbench
Human nuclear receptor liver receptor homologue-1, lrh-1, in its apo state bound to a fragment of human shp BOX1
Analyse Human nuclear receptor liver receptor homologue-1, lrh-1, in its apo state… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4DOR
- Type
- protein
- Length
- 478 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nuclear receptor subfamily 5 group a member 2; Nuclear receptor subfamily 0 group B…
- UniProt
- O00482, Q15466
- Ligands
- EPH
- Pockets
- 9 · best druggability 0.84
Structure
x-ray diffraction · 4 distinct chains · 73% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nuclear receptor subfamily 5 group a member 2 | protein | 216 | 75% helix, 0% strand | O00482 |
| B | Nuclear receptor subfamily 5 group a member 2 | protein | 240 | 70% helix, 3% strand | O00482 |
| C | Nuclear receptor subfamily 0 group B member 2 | protein | 12 | 67% helix, 0% strand | Q15466 |
| D | Nuclear receptor subfamily 0 group B member 2 | protein | 10 | 80% helix, 0% strand | Q15466 |
Ligands and binding sites
- EPH · L-alpha-phosphatidyl-beta-oleoyl-gamma-palmitoyl-phosphatidylethanolamine · ligand · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 613 | 0.84 | 0.88 | 51 | EPH |
| 2 | 132 | 0.76 | 0.94 | 25 | empty |
| 3 | 377 | 0.73 | 0.84 | 36 | empty |
| 4 | 148 | 0.70 | 0.89 | 22 | empty |
| 5 | 85 | 0.50 | 0.83 | 19 | empty |
Interfaces
3 interfaces between chains.
- A–B · 891 Ų buried · 22 hydrogen bonds · protein-protein
- A–C · 577 Ų buried · 8 hydrogen bonds · protein-protein
- B–D · 529 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 4DOR · Human Nuclear Receptor Liver Receptor Homologue-1, LRH-1, in its apo State Bound to 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 0.79
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 4DOR · PDBe 4DOR · UniProt O00482 · UniProt Q15466
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