MolNFT v1 · #95962 · protein
Crystal structure of the apo-PXR/RXRALPHA lbd heterotetramer complex
4J5W · Nuclear receptor subfamily 1 group I member 2, nuclear…: “Crystal structure of the apo-PXR/RXRALPHA lbd heterotetramer complex”. X-ray diffraction, 1 ligand (MG), 13 pockets (best druggability 0.86). MolNFT v1 #95962 on GenesisL1…
- PDB
- 4J5W
- Type
- protein
- Length
- 1,040 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nuclear receptor subfamily 1 group I member 2, nuclear receptor coactivator 1; Retinoic…
- EC
- 2.3.1.48
- UniProt
- O75469, Q15788, P19793
- Ligands
- MG
- Pockets
- 13 · best druggability 0.86
Structure
x-ray diffraction · 4 distinct chains · 62% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nuclear receptor subfamily 1 group I member 2, nuclear receptor coactivator 1 (EC 2.3.1.48) | protein | 294 | 58% helix, 7% strand | O75469, Q15788 |
| B | Nuclear receptor subfamily 1 group I member 2, nuclear receptor coactivator 1 (EC 2.3.1.48) | protein | 293 | 58% helix, 8% strand | O75469, Q15788 |
| C | Retinoic acid receptor rxr-alpha, nuclear receptor coactivator 1 (EC 2.3.1.48) | protein | 226 | 66% helix, 2% strand | Q15788, P19793 |
| D | Retinoic acid receptor rxr-alpha, nuclear receptor coactivator 1 (EC 2.3.1.48) | protein | 227 | 66% helix, 2% strand | Q15788, P19793 |
Ligands and binding sites
- MG · Magnesium ion · metal · 2 copies · chains C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 388 | 0.86 | 0.94 | 39 | empty |
| 2 | 347 | 0.86 | 0.95 | 34 | empty |
| 3 | 238 | 0.85 | 0.97 | 32 | empty |
| 4 | 329 | 0.83 | 0.93 | 52 | empty |
| 5 | 647 | 0.69 | 0.77 | 70 | empty |
Interfaces
3 interfaces between chains.
- B–C · 1302 Ų buried · 11 hydrogen bonds · protein-protein
- A–D · 1253 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 816 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 4J5W · Crystal Structure of the apo-PXR/RXRalpha LBD Heterotetramer Complex · 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 B against A, TM-score 0.93
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
- Every structure of UniProt Q15788
- Every structure of UniProt P19793
- Elsewhere: RCSB PDB 4J5W · PDBe 4J5W · UniProt O75469 · UniProt Q15788 · UniProt P19793
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