MolNFT v1 · #142030 · protein
Crystal structure of tetrameric rxralpha-lbd complexed with partial agonist cbt-pmn
5ZQU · Retinoic acid receptor rxr-alpha: “Crystal structure of tetrameric rxralpha-lbd complexed with partial agonist cbt-pmn”. X-ray diffraction, 2 ligands (9HF, BR), 7 pockets (best druggability 0.84). MolNFT v1 #142030 on GenesisL1: 3D…
- PDB
- 5ZQU
- Type
- protein
- Length
- 789 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Retinoic acid receptor rxr-alpha
- UniProt
- P19793
- Ligands
- 9HF, BR
- Pockets
- 7 · best druggability 0.84
Structure
x-ray diffraction · 4 distinct chains · 70% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Retinoic acid receptor rxr-alpha | protein | 198 | 69% helix, 3% strand | P19793 |
| B | Retinoic acid receptor rxr-alpha | protein | 198 | 70% helix, 3% strand | P19793 |
| C | Retinoic acid receptor rxr-alpha | protein | 197 | 71% helix, 3% strand | P19793 |
| D | Retinoic acid receptor rxr-alpha | protein | 196 | 69% helix, 3% strand | P19793 |
Ligands and binding sites
- 9HF · 1-(3,5,5,8,8-pentamethyl-6,7-dihydronaphthalen-2-yl) benzotriazole-5-carboxylic acid · ligand · 6 copies · chains A, C, B, D
- BR · Bromide ion · ion · 11 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 746 | 0.84 | 0.86 | 70 | 9HF |
| 2 | 681 | 0.83 | 0.86 | 63 | 9HF |
| 3 | 188 | 0.64 | 0.84 | 25 | BR |
| 4 | 99 | 0.64 | 0.89 | 25 | empty |
| 5 | 133 | 0.61 | 0.86 | 20 | empty |
Interfaces
4 interfaces between chains.
- A–C · 1560 Ų buried · 16 hydrogen bonds · protein-protein
- B–D · 1551 Ų buried · 16 hydrogen bonds · protein-protein
- C–D · 1212 Ų buried · 21 hydrogen bonds · protein-protein
- A–B · 1187 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 5ZQU · Crystal structure of tetrameric RXRalpha-LBD complexed with partial agonist CBt-PMN · 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 P19793
- Elsewhere: RCSB PDB 5ZQU · PDBe 5ZQU · UniProt P19793
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