Research workbench
Ligand complex of rorg lbd
Analyse Ligand complex of rorg lbd in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5APK
- Type
- protein
- Length
- 478 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nuclear receptor ror-gamma
- UniProt
- P51449
- Ligands
- 76E
- Pockets
- 7 · best druggability 0.83
Structure
x-ray diffraction · 3 distinct chains · 69% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nuclear receptor ror-gamma | protein | 229 | 71% helix, 4% strand | P51449 |
| B | Nuclear receptor ror-gamma | protein | 236 | 68% helix, 4% strand | P51449 |
| D | Nuclear receptor ror-gamma | protein | 13 | 62% helix, 0% strand | P51449 |
Ligands and binding sites
- 76E · 2-chloro-6-fluoro-N-[4-[3-(trifluoromethyl)phenyl]sulfonyl-3,5-dihydro-2H-1,4-benzoxazepin-7-yl]benzamide · ligand · 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 422 | 0.83 | 0.90 | 36 | 76E |
| 2 | 425 | 0.82 | 0.90 | 40 | 76E |
| 3 | 566 | 0.74 | 0.82 | 65 | empty |
| 4 | 174 | 0.51 | 0.78 | 19 | empty |
| 5 | 122 | 0.48 | 0.79 | 16 | empty |
Interfaces
3 interfaces between chains.
- A–D · 624 Ų buried · 7 hydrogen bonds · protein-protein
- B–D · 522 Ų buried · 1 hydrogen bond · protein-protein
- A–B · 413 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 5APK · Ligand complex of RORg LBD · 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
- Elsewhere: RCSB PDB 5APK · PDBe 5APK · UniProt P51449
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