Research workbench
Crystal structure of the human rxr DNA-binding domain homodimer bound to the human HOXB13 DR0 response element
Analyse Crystal structure of the human rxr DNA-binding domain homodimer bound to the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6XWH
- Type
- protein + DNA
- Length
- 190 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HOXB13 DR0 response element, 5'-3' strand; HOXB13 DR0 response element, 3'-5' strand…
- UniProt
- P19793
- Ligands
- ZN
- Pockets
- 5 · best druggability 0.56
Structure
x-ray diffraction · 4 distinct chains · 30% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | HOXB13 DR0 response element, 5'-3' strand | dna | 16 | — | — |
| B | HOXB13 DR0 response element, 3'-5' strand | dna | 16 | — | — |
| C | Retinoic acid receptor rxr-alpha | protein | 80 | 28% helix, 10% strand | P19793 |
| D | Retinoic acid receptor rxr-alpha | protein | 78 | 33% helix, 13% strand | P19793 |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 432 | 0.56 | 0.74 | 28 | empty |
| 2 | 159 | 0.50 | 0.78 | 19 | empty |
| 3 | 101 | 0.42 | 0.78 | 18 | empty |
| 4 | 50 | 0.26 | 0.74 | 17 | empty |
| 5 | 54 | 0.25 | 0.73 | 9 | empty |
Interfaces
5 interfaces between chains.
- A–B · 727 Ų buried · 75 hydrogen bonds · nucleic-nucleic
- A–C · 487 Ų buried · 15 hydrogen bonds · protein-nucleic
- B–C · 462 Ų buried · 13 hydrogen bonds · protein-nucleic
- A–D · 367 Ų buried · 8 hydrogen bonds · protein-nucleic
- B–D · 366 Ų buried · 11 hydrogen bonds · protein-nucleic
Compared structures
- 6XWH · Crystal Structure of the Human RXR DNA-Binding Domain Homodimer Bound to the Human Hoxb13… · the same entry in another collection · chain D against D, 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 6XWH · PDBe 6XWH · UniProt P19793
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