Research workbench
Crystal structure of rxralpha ligand-binding domain complexed with corepressor SMRT2
Analyse Crystal structure of rxralpha ligand-binding domain complexed with corepressor… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3R29
- Type
- protein
- Length
- 451 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Retinoic acid receptor rxr-alpha; Nuclear receptor corepressor 2
- UniProt
- P19793, Q9Y618
- Pockets
- 5 · best druggability 0.78
Structure
x-ray diffraction · 3 distinct chains · 63% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Retinoic acid receptor rxr-alpha | protein | 212 | 65% helix, 3% strand | P19793 |
| C | Nuclear receptor corepressor 2 | protein | 16 | 44% helix, 0% strand | Q9Y618 |
| D | Nuclear receptor corepressor 2 | protein | 11 | 64% helix, 0% strand | Q9Y618 |
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 793 | 0.78 | 0.82 | 75 | empty |
| 2 | 544 | 0.74 | 0.81 | 49 | empty |
| 3 | 125 | 0.68 | 0.89 | 25 | empty |
| 4 | 62 | 0.61 | 0.91 | 12 | empty |
| 5 | 102 | 0.49 | 0.81 | 26 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1268 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 562 Ų buried · 4 hydrogen bonds · protein-protein
- B–D · 469 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 3R29 · Crystal structure of RXRalpha ligand-binding domain complexed with corepressor SMRT2 · the same entry in another collection · chain A against A, TM-score 1.00
- Q9Y618 · AlphaFold monomer V2.0 prediction for nuclear receptor corepressor 2 (Q9Y618) · a predicted model of the same protein · chain D against A, TM-score 0.71
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 Q9Y618
- Elsewhere: RCSB PDB 3R29 · PDBe 3R29 · UniProt P19793 · UniProt Q9Y618
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