Research workbench
Glucocorticoid receptor with bound alaninamide 10 with TIF2 peptide
Analyse Glucocorticoid receptor with bound alaninamide 10 with TIF2 peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3K22
- Type
- protein
- Length
- 523 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glucocorticoid receptor; Transcriptional intermediary factor 2
- UniProt
- P04150
- Ligands
- JZR, JZS
- Pockets
- 3 · best druggability 0.85
Structure
x-ray diffraction · 4 distinct chains · 66% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glucocorticoid receptor | protein | 250 | 66% helix, 5% strand | P04150 |
| H | Transcriptional intermediary factor 2 | protein | 11 | 73% helix, 0% strand | — |
| B | Glucocorticoid receptor | protein | 250 | 66% helix, 5% strand | P04150 |
| D | Transcriptional intermediary factor 2 | protein | 12 | 67% helix, 0% strand | — |
Ligands and binding sites
- JZR · hexyl beta-D-glucopyranoside · ligand · 3 copies · chains A, B
- JZS · N-[(1R)-2-amino-1-methyl-2-oxoethyl]-3-(6-methyl-4-{[3,3,3-trifluoro-2-hydroxy-2-(trifluoromethyl)propyl]amino}-1H-indazol-1-yl)benzamide · ligand · 2 copies · chains A, B
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 | 350 | 0.85 | 0.94 | 46 | JZS, JZR |
| 2 | 837 | 0.80 | 0.82 | 97 | JZS, JZR |
| 3 | 60 | 0.28 | 0.74 | 19 | empty |
Interfaces
3 interfaces between chains.
- A–B · 709 Ų buried · 0 hydrogen bonds · protein-protein
- A–H · 591 Ų buried · 3 hydrogen bonds · protein-protein
- B–D · 554 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 3K22 · Glucocorticoid Receptor with Bound alaninamide 10 with TIF2 peptide · 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
- Elsewhere: RCSB PDB 3K22 · PDBe 3K22 · UniProt P04150
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