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
- 5NU1
- Type
- protein
- Length
- 507 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nuclear receptor ror-gamma; Nuclear receptor-interacting protein 1
- UniProt
- P51449, P48552
- Ligands
- 8YB
- Pockets
- 8 · best druggability 0.83
Structure
x-ray diffraction · 3 distinct chains · 71% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Nuclear receptor ror-gamma | protein | 245 | 71% helix, 4% strand | P51449 |
| P | Nuclear receptor-interacting protein 1 | protein | 8 | 75% helix, 0% strand | P48552 |
| Q | Nuclear receptor-interacting protein 1 | protein | 9 | 67% helix, 0% strand | P48552 |
Ligands and binding sites
- 8YB · ~{N}-[4-(3-chlorophenyl)-5-(2-chlorophenyl)carbonyl-1, 3-thiazol-2-yl]-2-(4-ethylsulfonylphenyl)ethanamide · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 352 | 0.83 | 0.91 | 36 | 8YB |
| 2 | 344 | 0.83 | 0.91 | 36 | 8YB |
| 3 | 566 | 0.67 | 0.77 | 61 | empty |
| 4 | 265 | 0.57 | 0.78 | 22 | empty |
| 5 | 191 | 0.51 | 0.77 | 21 | empty |
Interfaces
3 interfaces between chains.
- B–Q · 519 Ų buried · 3 hydrogen bonds · protein-protein
- A–P · 498 Ų buried · 3 hydrogen bonds · protein-protein
- A–B · 491 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 5NU1 · 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
- P48552 · AlphaFold monomer V2.0 prediction for nuclear receptor-interacting protein 1 (P48552) · a predicted model of the same protein · chain P against A, TM-score 0.87
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 P48552
- Elsewhere: RCSB PDB 5NU1 · PDBe 5NU1 · UniProt P51449 · UniProt P48552
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