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X-ray co-structure of nuclear receptor ror-gammat + SRC2 peptide with a benzothiadiazole dioxide inverse agonist
Analyse X-ray co-structure of nuclear receptor ror-gammat + SRC2 peptide with a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4YMQ
- Type
- protein
- Length
- 254 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nuclear receptor ror-gamma
- UniProt
- P51449
- Ligands
- ZBD, NA
- Pockets
- 4 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 72% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nuclear receptor ror-gamma | protein | 254 | 72% helix, 4% strand | P51449 |
Ligands and binding sites
- ZBD · 4-{3-[4-(1,1,1,3,3,3-hexafluoro-2-hydroxypropan-2-yl)benzyl]-2,2-dioxido-2,1,3-benzothiadiazol-1(3H)-yl}-N-[(2R)-4-hydroxybutan-2-yl]-N-methylbutanamide · ligand · chains A
- NA · Sodium ion · metal · chains A
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 430 | 0.83 | 0.90 | 36 | ZBD |
| 2 | 72 | 0.41 | 0.79 | 14 | NA |
| 3 | 99 | 0.39 | 0.75 | 13 | empty |
| 4 | 75 | 0.33 | 0.74 | 16 | empty |
Compared structures
- 4YMQ · X-ray co-structure of nuclear receptor ROR-GAMMAT + SRC2 peptide with a benzothiadiazole… · 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 4YMQ · PDBe 4YMQ · UniProt P51449
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