MolNFT v1 · #100698 · protein
Crystal structure of rxra lbd complexed with a synthetic modulator K8012
4N5G · Retinoic acid receptor rxr-alpha: “Crystal structure of rxra lbd complexed with a synthetic modulator K8012”. X-ray diffraction, 1 ligand (K09), 9 pockets (best druggability 0.84). MolNFT v1 #100698 on GenesisL1: 3D structure…
- PDB
- 4N5G
- Type
- protein
- Length
- 810 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Retinoic acid receptor rxr-alpha
- UniProt
- P19793
- Ligands
- K09
- Pockets
- 9 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 72% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Retinoic acid receptor rxr-alpha | protein | 196 | 73% helix, 4% strand | P19793 |
| B, C | Retinoic acid receptor rxr-alpha | protein | 209 | 72% helix, 3% strand | P19793 |
Ligands and binding sites
- K09 · 5-(2-{(1Z)-5-fluoro-2-methyl-1-[4-(propan-2-yl)benzylidene]-1H-inden-3-yl}ethyl)-1H-tetrazole · ligand · 2 copies · chains A, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 936 | 0.84 | 0.85 | 67 | K09 |
| 2 | 920 | 0.84 | 0.85 | 62 | K09 |
| 3 | 425 | 0.76 | 0.85 | 57 | empty |
| 4 | 204 | 0.66 | 0.85 | 30 | empty |
| 5 | 193 | 0.64 | 0.84 | 22 | empty |
Interfaces
4 interfaces between chains.
- A–C · 1375 Ų buried · 18 hydrogen bonds · protein-protein
- B–D · 1365 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 1174 Ų buried · 16 hydrogen bonds · protein-protein
- C–D · 1172 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 4N5G · Crystal Structure of RXRa LBD complexed with a synthetic modulator K8012 · 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 4N5G · PDBe 4N5G · UniProt P19793
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