MolNFT v1 · #174080 · protein
Crystal structure of rxralpha ligand binding domain in complex with a fragment of the TIF2 coactivator
7BK4 · Retinoic acid receptor rxr-alpha: “Crystal structure of rxralpha ligand binding domain in complex with a fragment of the TIF2 coactivator”. X-ray diffraction, 1 ligand (LG2), 5 pockets (best druggability 0.84). MolNFT v1 #174080 on…
- PDB
- 7BK4
- Type
- protein
- Length
- 462 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Retinoic acid receptor rxr-alpha; Nuclear receptor coactivator 2
- UniProt
- P19793, E7EWM1
- Ligands
- LG2
- Pockets
- 5 · best druggability 0.84
Structure
x-ray diffraction · 4 distinct chains · 69% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Retinoic acid receptor rxr-alpha | protein | 224 | 70% helix, 3% strand | P19793 |
| B | Nuclear receptor coactivator 2 | protein | 20 | 30% helix, 0% strand | E7EWM1 |
| C | Retinoic acid receptor rxr-alpha | protein | 210 | 72% helix, 3% strand | P19793 |
| D | Nuclear receptor coactivator 2 | protein | 8 | 63% helix, 0% strand | E7EWM1 |
Ligands and binding sites
- LG2 · 6-[1-(3,5,5,8,8-pentamethyl-5,6,7,8-tetrahydronaphthalen-2-yl)cyclopropyl]pyridine-3-carboxylic acid · ligand · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 226 | 0.84 | 0.96 | 29 | LG2 |
| 2 | 327 | 0.83 | 0.92 | 40 | LG2 |
| 3 | 242 | 0.54 | 0.77 | 30 | empty |
| 4 | 223 | 0.54 | 0.77 | 24 | empty |
| 5 | 57 | 0.52 | 0.87 | 18 | empty |
Interfaces
3 interfaces between chains.
- A–C · 1251 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 698 Ų buried · 7 hydrogen bonds · protein-protein
- C–D · 540 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 7BK4 · Crystal structure of RXRalpha ligand binding domain in complex with a fragment of the… · 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
- Every structure of UniProt E7EWM1
- Elsewhere: RCSB PDB 7BK4 · PDBe 7BK4 · UniProt P19793 · UniProt E7EWM1
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