Research workbench
Crystal structure of the glucocorticoid receptor ligand binding domain bound to a dibenzoxapine sulfonamide
Analyse Crystal structure of the glucocorticoid receptor ligand binding domain bound to… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4LSJ
- Type
- protein
- Length
- 254 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glucocorticoid receptor; D30 peptide
- UniProt
- P04150
- Ligands
- LSJ
- Pockets
- 3 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 67% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glucocorticoid receptor | protein | 244 | 67% helix, 6% strand | P04150 |
| B | D30 peptide | protein | 10 | 80% helix, 0% strand | — |
Ligands and binding sites
- LSJ · N-{3-[(1Z)-1-(10-methoxydibenzo[b,e]oxepin-11(6H)-ylidene)propyl]phenyl}methanesulfonamide · ligand · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 277 | 0.83 | 0.93 | 33 | LSJ |
| 2 | 59 | 0.51 | 0.86 | 17 | empty |
| 3 | 59 | 0.35 | 0.77 | 12 | empty |
Interfaces
1 interface between chains.
- A–B · 564 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 4LSJ · Crystal Structure of the Glucocorticoid Receptor Ligand Binding Domain Bound to a… · 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 0.87
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 P04150
- Elsewhere: RCSB PDB 4LSJ · PDBe 4LSJ · UniProt P04150
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