Research workbench
The crystal structure of human liver receptor homologue-1
Analyse The crystal structure of human liver receptor homologue-1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1ZDU
- Type
- protein
- Length
- 254 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
- P3A
- Pockets
- 3 · best druggability 0.85
Structure
x-ray diffraction · 3 distinct chains · 70% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Orphan nuclear receptor NR5A2 | protein | 233 | 70% helix, 3% strand | O00482 |
| P | Nuclear receptor coactivator 2 | protein | 11 | 73% helix, 0% strand | Q15596 |
| Q | Nuclear receptor coactivator 2 | protein | 10 | 80% helix, 0% strand | Q15596 |
Ligands and binding sites
- P3A · Phosphatidylglycerol-phosphoglycerol · ligand · chains A
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 592 | 0.85 | 0.89 | 42 | P3A |
| 2 | 97 | 0.67 | 0.91 | 21 | TRS |
| 3 | 62 | 0.31 | 0.75 | 14 | empty |
Interfaces
2 interfaces between chains.
- A–P · 642 Ų buried · 10 hydrogen bonds · protein-protein
- A–Q · 464 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 1ZDU · The Crystal Structure of Human Liver Receptor Homologue-1 · 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 1ZDU · PDBe 1ZDU · UniProt O00482 · UniProt Q15596
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