Research workbench
Doubling the size of the glucocorticoid receptor ligand binding pocket by deacylcortivazol
Analyse Doubling the size of the glucocorticoid receptor ligand binding pocket by… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3BQD
- Type
- protein
- Length
- 264 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glucocorticoid receptor; Nuclear receptor coactivator 1
- EC
- 2.3.1.48
- UniProt
- P04150, Q15788
- Ligands
- DAY
- Pockets
- 1 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 64% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glucocorticoid receptor | protein | 253 | 65% helix, 5% strand | P04150 |
| B | Nuclear receptor coactivator 1 (EC 2.3.1.48) | protein | 11 | 45% helix, 0% strand | Q15788 |
Ligands and binding sites
- DAY · 1-[(1R,2R,3aS,3bS,10aR,10bS,11S,12aS)-1,11-dihydroxy-2,5,10a,12a-tetramethyl-7-phenyl-1,2,3,3a,3b,7,10,10a,10b,11,12,12a-dodecahydrocyclopenta[5,6]naphtho[1,2-f]indazol-1-yl]-2-hydroxyethanone · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 315 | 0.86 | 0.95 | 40 | DAY |
Interfaces
1 interface between chains.
- A–B · 544 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 3BQD · Doubling the Size of the Glucocorticoid Receptor Ligand Binding Pocket by Deacylcortivazol · the same entry in another collection · chain A against A, TM-score 1.00
- P04150 · AlphaFold monomer V2.0 prediction for glucocorticoid receptor (P04150) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 P04150
- Every structure of UniProt Q15788
- Elsewhere: RCSB PDB 3BQD · PDBe 3BQD · UniProt P04150 · UniProt Q15788
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