MolNFT v1 · #88182 · protein + DNA
Crystal structure of the human retinoid X receptor DNA- binding domain bound to the human GDE1SPA response element
4CN3 · Retinoic acid receptor rxr-alpha: “Crystal structure of the human retinoid X receptor DNA- binding domain bound to the human GDE1SPA response…”. X-ray diffraction, 1 ligand (ZN), 9 pockets (best druggability 0.63). MolNFT v1 #88182…
- PDB
- 4CN3
- Type
- protein + DNA
- Length
- 384 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Retinoic acid receptor rxr-alpha; 5'-D(*CP*TP*AP*GP*TP*TP*CP*AP*AP*AP*GP*TP*TP*CP…
- UniProt
- P19793
- Ligands
- ZN
- Pockets
- 9 · best druggability 0.63
Structure
x-ray diffraction · 6 distinct chains · 34% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Retinoic acid receptor rxr-alpha | protein | 78 | 35% helix, 8% strand | P19793 |
| B | Retinoic acid receptor rxr-alpha | protein | 76 | 33% helix, 11% strand | P19793 |
| C | Retinoic acid receptor rxr-alpha | protein | 84 | 33% helix, 10% strand | P19793 |
| D | Retinoic acid receptor rxr-alpha | protein | 78 | 35% helix, 8% strand | P19793 |
| E, G | 5'-D(*CP*TP*AP*GP*TP*TP*CP*AP*AP*AP*GP*TP*TP*CP *AP*CP*A)-3' | dna | 17 | — | — |
| F, H | 5'-D(*TP*GP*TP*GP*AP*AP*CP*TP*TP*TP*GP*AP*AP*CP *TP*AP*G)-3' | dna | 17 | — | — |
Ligands and binding sites
- ZN · Zinc ion · metal · 8 copies · chains A, B, 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 572 | 0.63 | 0.75 | 53 | empty |
| 2 | 281 | 0.52 | 0.75 | 36 | empty |
| 3 | 213 | 0.51 | 0.77 | 25 | empty |
| 4 | 233 | 0.51 | 0.76 | 22 | empty |
| 5 | 126 | 0.42 | 0.76 | 18 | empty |
Interfaces
14 interfaces between chains.
- G–H · 670 Ų buried · 66 hydrogen bonds · nucleic-nucleic
- E–F · 668 Ų buried · 59 hydrogen bonds · nucleic-nucleic
- C–G · 459 Ų buried · 11 hydrogen bonds · protein-nucleic
- D–E · 451 Ų buried · 11 hydrogen bonds · protein-nucleic
- D–F · 448 Ų buried · 12 hydrogen bonds · protein-nucleic
Compared structures
- 4CN3 · Crystal Structure of the Human Retinoid X Receptor DNA-Binding Domain Bound to the Human… · 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 4CN3 · PDBe 4CN3 · UniProt P19793
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