MolNFT v1 · #27405 · protein
Crystal structure of the agonist-bound ligand-binding domain of biomphalaria glabrata rxr
1XIU · Rxr-like protein: “Crystal structure of the agonist-bound ligand-binding domain of biomphalaria glabrata rxr”. X-ray diffraction, 1 ligand (9CR), 6 pockets (best druggability 0.83). MolNFT v1 #27405 on GenesisL1: 3D structure…
- PDB
- 1XIU
- Type
- protein
- Length
- 467 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Rxr-like protein; Nuclear receptor coactivator 1
- EC
- 2.3.1.48
- UniProt
- Q15788
- Ligands
- 9CR
- Pockets
- 6 · best druggability 0.83
Structure
x-ray diffraction · 4 distinct chains · 69% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Rxr-like protein | protein | 221 | 69% helix, 5% strand | — |
| B | Rxr-like protein | protein | 224 | 68% helix, 4% strand | — |
| E | Nuclear receptor coactivator 1 (EC 2.3.1.48) | protein | 12 | 75% helix, 0% strand | Q15788 |
| F | Nuclear receptor coactivator 1 (EC 2.3.1.48) | protein | 10 | 60% helix, 0% strand | Q15788 |
Ligands and binding sites
- 9CR · (9cis)-retinoic acid · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 305 | 0.83 | 0.93 | 47 | 9CR |
| 2 | 337 | 0.80 | 0.90 | 46 | 9CR |
| 3 | 513 | 0.67 | 0.78 | 46 | empty |
| 4 | 65 | 0.54 | 0.87 | 11 | empty |
| 5 | 140 | 0.50 | 0.78 | 13 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1126 Ų buried · 11 hydrogen bonds · protein-protein
- B–F · 490 Ų buried · 6 hydrogen bonds · protein-protein
- A–E · 475 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 1XIU · Crystal structure of the agonist-bound ligand-binding domain of Biomphalaria glabrata RXR · the same entry in another collection · chain A against A, TM-score 1.00
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 Q15788
- Elsewhere: RCSB PDB 1XIU · PDBe 1XIU · UniProt Q15788
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