MolNFT v1 · #170093 · protein + DNA
Crystal structure of the human RXR/RAR DNA-binding domain heterodimer bound to the human RARB2 DR5 response element
6XWG · RARB2 DR5 response element, 5'-3' strand: “Crystal structure of the human RXR/RAR DNA-binding domain heterodimer bound to the human RARB2 DR5 response…”. X-ray diffraction, 2 ligands (ZN, CL), 5 pockets (best druggability 0.68).…
- PDB
- 6XWG
- Type
- protein + DNA
- Length
- 201 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RARB2 DR5 response element, 5'-3' strand; RARB2 DR5 response element, 3'-5' strand…
- UniProt
- P19793, P10276
- Ligands
- ZN, CL
- Pockets
- 5 · best druggability 0.68
Structure
x-ray diffraction · 4 distinct chains · 32% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RARB2 DR5 response element, 5'-3' strand | dna | 21 | — | — |
| B | RARB2 DR5 response element, 3'-5' strand | dna | 21 | — | — |
| C | Retinoic acid receptor rxr-alpha | protein | 79 | 32% helix, 13% strand | P19793 |
| D | Retinoic acid receptor alpha | protein | 80 | 33% helix, 8% strand | P10276 |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains C, D
- CL · Chloride ion · ion · chains C
- GOL · Glycerol · additive · chains 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 677 | 0.68 | 0.77 | 41 | empty |
| 2 | 91 | 0.43 | 0.79 | 22 | empty |
| 3 | 84 | 0.33 | 0.75 | 15 | empty |
| 4 | 89 | 0.32 | 0.73 | 11 | empty |
| 5 | 50 | 0.26 | 0.74 | 19 | empty |
Interfaces
6 interfaces between chains.
- A–B · 946 Ų buried · 96 hydrogen bonds · nucleic-nucleic
- A–C · 542 Ų buried · 16 hydrogen bonds · protein-nucleic
- B–D · 419 Ų buried · 13 hydrogen bonds · protein-nucleic
- B–C · 399 Ų buried · 13 hydrogen bonds · protein-nucleic
- A–D · 378 Ų buried · 6 hydrogen bonds · protein-nucleic
Compared structures
- 6XWG · Crystal Structure of the Human RXR/RAR DNA-Binding Domain Heterodimer Bound to the Human… · the same entry in another collection · chain A against A, TM-score 1.00
- P10276 · AlphaFold monomer V2.0 prediction for retinoic acid receptor alpha (P10276) · a predicted model of the same protein · chain D against A, TM-score 0.96
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 P10276
- Elsewhere: RCSB PDB 6XWG · PDBe 6XWG · UniProt P19793 · UniProt P10276
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