Research workbench
Crystal structure of the mutant human ror gamma ligand binding domain with compound a.
Analyse Crystal structure of the mutant human ror gamma ligand binding domain with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5X8X
- Type
- protein
- Length
- 965 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nuclear receptor ror-gamma; Nuclear receptor corepressor 2
- UniProt
- P51449, Q9Y618
- Ligands
- 82O
- Pockets
- 17 · best druggability 0.84
Structure
x-ray diffraction · 5 distinct chains · 72% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E | Nuclear receptor ror-gamma | protein | 228 | 71% helix, 4% strand | P51449 |
| B | Nuclear receptor corepressor 2 | protein | 13 | 85% helix, 0% strand | Q9Y618 |
| D, H | Nuclear receptor corepressor 2 | protein | 15 | 80% helix, 0% strand | Q9Y618 |
| F | Nuclear receptor corepressor 2 | protein | 14 | 79% helix, 0% strand | Q9Y618 |
| G | Nuclear receptor ror-gamma | protein | 224 | 72% helix, 4% strand | P51449 |
Ligands and binding sites
- 82O · (3R,4R)-4-[4-cyclopropyl-5-[3-(2-methylpropyl) cyclobutyl]-1,2,4-triazol-3-yl]-N-(2,4-dimethylphenyl)-1-ethanoyl-pyrrolidine-3-carboxamide · ligand · 4 copies · chains A, C, E, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 463 | 0.84 | 0.90 | 35 | 82O |
| 2 | 459 | 0.83 | 0.90 | 35 | 82O |
| 3 | 471 | 0.83 | 0.89 | 34 | 82O |
| 4 | 387 | 0.82 | 0.90 | 35 | 82O |
| 5 | 829 | 0.78 | 0.81 | 78 | empty |
Interfaces
11 interfaces between chains.
- C–D · 776 Ų buried · 7 hydrogen bonds · protein-protein
- C–G · 775 Ų buried · 11 hydrogen bonds · protein-protein
- G–H · 759 Ų buried · 8 hydrogen bonds · protein-protein
- E–F · 758 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 703 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 5X8X · Crystal Structure of the mutant Human ROR gamma Ligand Binding Domain With Compound A. · the same entry in another collection · chain H against H, TM-score 1.00
- Q9Y618 · AlphaFold monomer V2.0 prediction for nuclear receptor corepressor 2 (Q9Y618) · a predicted model of the same protein · chain B against A, TM-score 0.72
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 Q9Y618
- Elsewhere: RCSB PDB 5X8X · PDBe 5X8X · UniProt P51449 · UniProt Q9Y618
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