MolNFT v1 · #148613 · protein + DNA
Crystal structure of the human retinoid X receptor DNA-binding domain bound to the human mep DR1 response element, pH 4.2
6FBR · Retinoic acid receptor rxr-alpha: “Crystal structure of the human retinoid X receptor DNA-binding domain bound to the human mep DR1 response…”. X-ray diffraction, 2 ligands (ZN, PO4), 6 pockets (best druggability 0.52). MolNFT v1…
- PDB
- 6FBR
- Type
- protein + DNA
- Length
- 193 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Retinoic acid receptor rxr-alpha; DNA (5'- D(*CP*TP*GP*GP*GP*TP*CP*AP*AP*AP*GP*TP*TP*CP*AP…
- UniProt
- P19793
- Ligands
- ZN, PO4
- Pockets
- 6 · best druggability 0.52
Structure
x-ray diffraction · 4 distinct chains · 34% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Retinoic acid receptor rxr-alpha | protein | 78 | 35% helix, 13% strand | P19793 |
| B | Retinoic acid receptor rxr-alpha | protein | 81 | 33% helix, 10% strand | P19793 |
| C | DNA (5'- D(*CP*TP*GP*GP*GP*TP*CP*AP*AP*AP*GP*TP*TP*CP*AP*TP*C)-3') | dna | 17 | — | — |
| D | DNA (5'- D(*GP*AP*TP*GP*AP*AP*CP*TP*TP*TP*GP*AP*CP*CP*CP*AP*G)-3') | dna | 17 | — | — |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains A, B
- PO4 · Phosphate ion · ion · chains B, C, D
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains B, C
- PGE · Triethylene glycol · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 247 | 0.52 | 0.76 | 25 | empty |
| 2 | 99 | 0.42 | 0.78 | 16 | empty |
| 3 | 89 | 0.40 | 0.78 | 20 | empty |
| 4 | 92 | 0.35 | 0.75 | 17 | empty |
| 5 | 58 | 0.29 | 0.75 | 18 | empty |
Interfaces
6 interfaces between chains.
- C–D · 766 Ų buried · 75 hydrogen bonds · nucleic-nucleic
- B–C · 568 Ų buried · 15 hydrogen bonds · protein-nucleic
- B–D · 477 Ų buried · 14 hydrogen bonds · protein-nucleic
- A–C · 416 Ų buried · 14 hydrogen bonds · protein-nucleic
- A–D · 387 Ų buried · 12 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 6FBR · 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 6FBR · PDBe 6FBR · UniProt P19793
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