Research workbench
Structure and mechanism of the homodimeric assembly of the rxr on DNA
Analyse Structure and mechanism of the homodimeric assembly of the rxr on DNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1BY4
- Type
- protein + DNA
- Length
- 380 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein (retinoic acid receptor rxr-alpha); DNA (5'…
- UniProt
- P19793
- Ligands
- ZN
- Pockets
- 10 · best druggability 0.62
Structure
x-ray diffraction · 7 distinct chains · 32% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein (retinoic acid receptor rxr-alpha) | protein | 79 | 30% helix, 5% strand | P19793 |
| B | Protein (retinoic acid receptor rxr-alpha) | protein | 82 | 32% helix, 10% strand | P19793 |
| C | Protein (retinoic acid receptor rxr-alpha) | protein | 78 | 29% helix, 5% strand | P19793 |
| D | Protein (retinoic acid receptor rxr-alpha) | protein | 80 | 36% helix, 10% strand | P19793 |
| E | DNA (5'- D(*C*TP*AP*GP*GP*TP*CP*AP*AP*AP*GP*GP*TP*CP*AP*G)-3') | dna | 15 | — | — |
| F, H | DNA (5'- D(*CP*TP*GP*AP*CP*CP*TP*TP*TP*GP*AP*CP*CP*TP*A)-3') | dna | 15 | — | — |
| G | DNA (5'- D(*C*TP*AP*GP*GP*TP*CP*AP*AP*AP*GP*GP*TP*CP*AP*G)-3') | dna | 16 | — | — |
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
10 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 370 | 0.62 | 0.78 | 34 | empty |
| 2 | 351 | 0.58 | 0.77 | 29 | empty |
| 3 | 345 | 0.55 | 0.75 | 30 | empty |
| 4 | 84 | 0.41 | 0.79 | 19 | empty |
| 5 | 127 | 0.40 | 0.75 | 20 | empty |
Interfaces
18 interfaces between chains.
- E–F · 689 Ų buried · 77 hydrogen bonds · nucleic-nucleic
- G–H · 687 Ų buried · 64 hydrogen bonds · nucleic-nucleic
- B–E · 436 Ų buried · 11 hydrogen bonds · protein-nucleic
- B–F · 404 Ų buried · 13 hydrogen bonds · protein-nucleic
- D–G · 395 Ų buried · 9 hydrogen bonds · protein-nucleic
Compared structures
- 1BY4 · Structure and mechanism of the homodimeric assembly of the rxr on DNA · the same entry in another collection · chain E against E, 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 1BY4 · PDBe 1BY4 · UniProt P19793
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