MolNFT v1 · #88186 · protein + DNA
Crystal structure of the human retinoid X receptor DNA- binding domain bound to an idealized DR1 response element
4CN7 · Retinoic acid receptor rxr-alpha: “Crystal structure of the human retinoid X receptor DNA- binding domain bound to an idealized DR1 response…”. X-ray diffraction, 2 ligands (ZN, CL), 7 pockets (best druggability 0.76). MolNFT v1…
- PDB
- 4CN7
- Type
- protein + DNA
- Length
- 379 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*GP*TP*CP*AP*AP*AP*GP*GP*TP*CP…
- UniProt
- P19793
- Ligands
- ZN, CL
- Pockets
- 7 · best druggability 0.76
Structure
x-ray diffraction · 6 distinct chains · 37% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Retinoic acid receptor rxr-alpha | protein | 79 | 37% helix, 8% strand | P19793 |
| B | Retinoic acid receptor rxr-alpha | protein | 79 | 37% helix, 13% strand | P19793 |
| C, G | 5'-D(*CP*TP*AP*GP*GP*TP*CP*AP*AP*AP*GP*GP*TP*CP *AP*GP)-3' | dna | 16 | — | — |
| D, H | 5'-D(*CP*TP*GP*AP*CP*CP*TP*TP*TP*GP*AP*CP*CP*TP *AP*GP)-3' | dna | 16 | — | — |
| E | Retinoic acid receptor rxr-alpha | protein | 77 | 39% helix, 8% strand | P19793 |
| F | Retinoic acid receptor rxr-alpha | protein | 80 | 36% helix, 8% strand | P19793 |
Ligands and binding sites
- ZN · Zinc ion · metal · 8 copies · chains A, B, E, F
- CL · Chloride ion · ion · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 984 | 0.76 | 0.79 | 85 | empty |
| 2 | 131 | 0.46 | 0.78 | 19 | empty |
| 3 | 125 | 0.45 | 0.78 | 16 | empty |
| 4 | 167 | 0.44 | 0.75 | 21 | empty |
| 5 | 171 | 0.44 | 0.75 | 22 | empty |
Interfaces
21 interfaces between chains.
- C–D · 741 Ų buried · 82 hydrogen bonds · nucleic-nucleic
- G–H · 736 Ų buried · 73 hydrogen bonds · nucleic-nucleic
- B–D · 476 Ų buried · 14 hydrogen bonds · protein-nucleic
- F–G · 471 Ų buried · 12 hydrogen bonds · protein-nucleic
- B–C · 466 Ų buried · 13 hydrogen bonds · protein-nucleic
Compared structures
- 4CN7 · Crystal Structure of the Human Retinoid X Receptor DNA-Binding Domain Bound to an… · 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 4CN7 · PDBe 4CN7 · UniProt P19793
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