Research workbench
Crystal structure of the orphan nuclear receptor roralpha ligand- binding domain in complex with 4ALPHA-caboxyl, 4BETA-methyl- zymosterol (4ACD8)
Analyse Crystal structure of the orphan nuclear receptor roralpha ligand- binding… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4S15
- Type
- protein
- Length
- 512 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nuclear receptor ror-alpha; Nuclear receptor-interacting protein 1
- UniProt
- P35398, P48552
- Ligands
- 4D8
- Pockets
- 7 · best druggability 0.83
Structure
x-ray diffraction · 3 distinct chains · 72% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nuclear receptor ror-alpha | protein | 244 | 75% helix, 4% strand | P35398 |
| C, D | Nuclear receptor-interacting protein 1 | protein | 9 | 67% helix, 0% strand | P48552 |
| B | Nuclear receptor ror-alpha | protein | 250 | 70% helix, 4% strand | P35398 |
Ligands and binding sites
- 4D8 · (3beta,4alpha,5beta,14beta)-3-hydroxy-4-methylcholesta-8,24-diene-4-carboxylic acid · ligand · 2 copies · chains A, B
- GOL · Glycerol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 484 | 0.83 | 0.89 | 50 | 4D8, GOL |
| 2 | 447 | 0.83 | 0.89 | 45 | 4D8, GOL |
| 3 | 73 | 0.74 | 0.98 | 23 | empty |
| 4 | 131 | 0.49 | 0.79 | 16 | empty |
| 5 | 234 | 0.49 | 0.74 | 28 | empty |
Interfaces
6 interfaces between chains.
- A–B · 722 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 481 Ų buried · 6 hydrogen bonds · protein-protein
- B–D · 469 Ų buried · 7 hydrogen bonds · protein-protein
- C–B · 257 Ų buried · 0 hydrogen bonds · protein-protein
- A–D · 257 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4S15 · Crystal structure of the orphan nuclear receptor RORalpha ligand-binding domain in… · the same entry in another collection · chain A against A, TM-score 1.00
- P35398 · AlphaFold monomer V2.0 prediction for nuclear receptor ror-alpha (P35398) · a predicted model of the same protein · chain A against A, TM-score 0.98
- P48552 · AlphaFold monomer V2.0 prediction for nuclear receptor-interacting protein 1 (P48552) · a predicted model of the same protein · chain C against A, TM-score 0.80
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 P35398
- Every structure of UniProt P48552
- Elsewhere: RCSB PDB 4S15 · PDBe 4S15 · UniProt P35398 · UniProt P48552
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