MolNFT v1 · #16192 · protein
Crystal structure of the human pxr-lbd in complex with an src-1 coactivator peptide and SR12813
1NRL · Orphan nuclear receptor pxr: “Crystal structure of the human pxr-lbd in complex with an src-1 coactivator peptide and SR12813”. X-ray diffraction, 1 ligand (SRL), 5 pockets (best druggability 0.87). MolNFT v1 #16192 on GenesisL1: 3D…
- PDB
- 1NRL
- Type
- protein
- Length
- 583 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Orphan nuclear receptor pxr; Nuclear receptor coactivator 1 isoform 3
- UniProt
- O75469
- Ligands
- SRL
- Pockets
- 5 · best druggability 0.87
Structure
x-ray diffraction · 3 distinct chains · 60% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Orphan nuclear receptor pxr | protein | 278 | 61% helix, 8% strand | O75469 |
| B | Orphan nuclear receptor pxr | protein | 275 | 60% helix, 8% strand | O75469 |
| C, D | Nuclear receptor coactivator 1 isoform 3 | protein | 15 | 47% helix, 0% strand | — |
Ligands and binding sites
- SRL · [2-(3,5-di-tert-butyl-4-hydroxy-phenyl)-1-(diethoxy-phosphoryl)-vinyl]-phosphonic acid diethlyl ester · ligand · 2 copies · chains A, B
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 | 491 | 0.87 | 0.93 | 41 | SRL |
| 2 | 483 | 0.87 | 0.93 | 43 | SRL |
| 3 | 70 | 0.36 | 0.77 | 15 | empty |
| 4 | 80 | 0.32 | 0.74 | 14 | empty |
| 5 | 78 | 0.31 | 0.74 | 14 | empty |
Interfaces
3 interfaces between chains.
- A–B · 792 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 618 Ų buried · 8 hydrogen bonds · protein-protein
- B–D · 606 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 1NRL · Crystal Structure of the human PXR-LBD in complex with an SRC-1 coactivator peptide and… · the same entry in another collection · chain A against A, TM-score 1.00
- O75469 · AlphaFold monomer V2.0 prediction for nuclear receptor subfamily 1 group I member 2… · a predicted model of the same protein · chain A against A, TM-score 0.99
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 O75469
- Elsewhere: RCSB PDB 1NRL · PDBe 1NRL · UniProt O75469
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