Research workbench
Crystal structure of the human retinoid X receptor DNA- binding domain bound to the human NR1D1 response element
Analyse Crystal structure of the human retinoid X receptor DNA- binding domain bound to… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4CN5
- Type
- protein + DNA
- Length
- 190 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Retinoic acid receptor rxr-alpha; 5'-D(*TP*GP*GP*GP*GP*TP*CP*AP*GP*AP*GP*TP*TP*CP…
- UniProt
- P19793
- Ligands
- ZN, K, CL, NO3
- Pockets
- 5 · best druggability 0.46
Structure
x-ray diffraction · 4 distinct chains · 34% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Retinoic acid receptor rxr-alpha | protein | 81 | 31% helix, 12% strand | P19793 |
| B | Retinoic acid receptor rxr-alpha | protein | 75 | 37% helix, 8% strand | P19793 |
| C | 5'-D(*TP*GP*GP*GP*GP*TP*CP*AP*GP*AP*GP*TP*TP*CP *AP*AP*TP)-3' | dna | 17 | — | — |
| D | 5'-D(*AP*TP*TP*GP*AP*AP*CP*TP*CP*TP*GP*AP*CP*CP *CP*CP*AP)-3' | dna | 17 | — | — |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains A, B
- K · Potassium ion · metal · 4 copies · chains C, D
- CL · Chloride ion · ion · 5 copies · chains A, B, C, D
- NO3 · Nitrate ion · ion · chains B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 152 | 0.46 | 0.77 | 22 | CL |
| 2 | 167 | 0.44 | 0.75 | 23 | K, NO3 |
| 3 | 89 | 0.40 | 0.78 | 15 | empty |
| 4 | 82 | 0.39 | 0.78 | 20 | empty |
| 5 | 55 | 0.28 | 0.75 | 13 | CL |
Interfaces
6 interfaces between chains.
- C–D · 766 Ų buried · 69 hydrogen bonds · nucleic-nucleic
- A–C · 482 Ų buried · 11 hydrogen bonds · protein-nucleic
- B–D · 461 Ų buried · 13 hydrogen bonds · protein-nucleic
- B–C · 441 Ų buried · 11 hydrogen bonds · protein-nucleic
- A–D · 434 Ų buried · 13 hydrogen bonds · protein-nucleic
Compared structures
- 4CN5 · 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 4CN5 · PDBe 4CN5 · UniProt P19793
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