Research workbench
Crystal structure of orphan nuclear receptor rorgamma in complex with natural ligand
Analyse Crystal structure of orphan nuclear receptor rorgamma in complex with natural… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3L0L
- Type
- protein
- Length
- 518 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nuclear receptor ror-gamma; SCR2-2
- UniProt
- P51449, Q15596
- Ligands
- HC3
- Pockets
- 9 · best druggability 0.89
Structure
x-ray diffraction · 4 distinct chains · 70% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nuclear receptor ror-gamma | protein | 247 | 72% helix, 4% strand | P51449 |
| C | SCR2-2 | protein | 13 | 54% helix, 0% strand | Q15596 |
| B | Nuclear receptor ror-gamma | protein | 248 | 69% helix, 4% strand | P51449 |
| E | SCR2-2 | protein | 10 | 70% helix, 0% strand | Q15596 |
Ligands and binding sites
- HC3 · 25-hydroxycholesterol · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1196 | 0.89 | 0.90 | 98 | HC3 |
| 2 | 232 | 0.54 | 0.77 | 22 | empty |
| 3 | 143 | 0.52 | 0.80 | 21 | empty |
| 4 | 100 | 0.48 | 0.80 | 16 | empty |
| 5 | 71 | 0.41 | 0.79 | 20 | empty |
Interfaces
5 interfaces between chains.
- A–B · 935 Ų buried · 18 hydrogen bonds · protein-protein
- A–C · 653 Ų buried · 11 hydrogen bonds · protein-protein
- B–E · 520 Ų buried · 6 hydrogen bonds · protein-protein
- A–E · 223 Ų buried · 2 hydrogen bonds · protein-protein
- C–B · 205 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 3L0L · Crystal structure of orphan nuclear receptor RORgamma in complex with natural ligand · 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 P51449
- Every structure of UniProt Q15596
- Elsewhere: RCSB PDB 3L0L · PDBe 3L0L · UniProt P51449 · UniProt Q15596
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