MolNFT v1 · #134664 · protein
Crystal structure of rxr-alpha ligand binding domain complexed with synthetic modulator K8003
5TBP · Retinoic acid receptor rxr-alpha: “Crystal structure of rxr-alpha ligand binding domain complexed with synthetic modulator K8003”. X-ray diffraction, 1 ligand (7A4), 9 pockets (best druggability 0.87). MolNFT v1 #134664 on…
- PDB
- 5TBP
- Type
- protein
- Length
- 822 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Retinoic acid receptor rxr-alpha
- UniProt
- P19793
- Ligands
- 7A4
- Pockets
- 9 · best druggability 0.87
Structure
x-ray diffraction · 3 distinct chains · 70% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Retinoic acid receptor rxr-alpha | protein | 198 | 71% helix, 3% strand | P19793 |
| B | Retinoic acid receptor rxr-alpha | protein | 213 | 69% helix, 3% strand | P19793 |
| C | Retinoic acid receptor rxr-alpha | protein | 213 | 69% helix, 3% strand | P19793 |
Ligands and binding sites
- 7A4 · [(1Z)-5-fluoro-2-methyl-1-{[4-(propan-2-yl) phenyl]methylidene}-1H-inden-3-yl]acetic acid · ligand · 6 copies · chains A, C, B, D
- ACT · Acetate ion · additive · 7 copies · chains A, B, D
- GOL · Glycerol · additive · 2 copies · chains B, C
- DMS · Dimethyl sulfoxide · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 992 | 0.87 | 0.87 | 93 | 7A4, GOL |
| 2 | 856 | 0.85 | 0.87 | 71 | 7A4, GOL, ACT |
| 3 | 158 | 0.67 | 0.87 | 30 | empty |
| 4 | 51 | 0.60 | 0.92 | 13 | ACT |
| 5 | 103 | 0.58 | 0.86 | 16 | empty |
Interfaces
5 interfaces between chains.
- A–C · 1539 Ų buried · 17 hydrogen bonds · protein-protein
- B–D · 1493 Ų buried · 13 hydrogen bonds · protein-protein
- C–D · 1232 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 1216 Ų buried · 19 hydrogen bonds · protein-protein
- A–D · 27 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 5TBP · Crystal Structure of RXR-alpha ligand binding domain complexed with synthetic modulator… · 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 5TBP · PDBe 5TBP · UniProt P19793
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