Research workbench
Structural states of rorgt: X-ray elucidation of molecular mechanisms and binding interactions for natural and synthetic compounds
Analyse Structural states of rorgt: X-ray elucidation of molecular mechanisms and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5NTK
- Type
- protein
- Length
- 450 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nuclear receptor ror-gamma
- UniProt
- P51449
- Ligands
- 99N
- Pockets
- 6 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 70% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Nuclear receptor ror-gamma | protein | 225 | 70% helix, 4% strand | P51449 |
Ligands and binding sites
- 99N · [(3~{S},8~{S},9~{S},10~{R},13~{R},14~{S},17~{R})-10,13-dimethyl-17-[(2~{R})-5-[[4-(2-morpholin-4-ylethoxy) phenyl]methylamino]-5-oxidanylidene-pentan-2-yl]-2,3, 4,7,8,9,11,12,14,15,16,17-dodecahydro-1~{H}-cyclopenta[a]phenanthren-3-yl] hydrogen sulfate · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 481 | 0.83 | 0.89 | 39 | 99N |
| 2 | 552 | 0.83 | 0.88 | 48 | 99N |
| 3 | 496 | 0.64 | 0.77 | 50 | empty |
| 4 | 65 | 0.54 | 0.88 | 20 | empty |
| 5 | 181 | 0.49 | 0.76 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 607 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 5NTK · Structural states of RORgt: X-ray elucidation of molecular mechanisms and binding… · 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 5NTK · PDBe 5NTK · UniProt P51449
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.