Research workbench
The glucocorticoid receptor in complex with velsecorat, a PGC1a coactivator fragment and sgk 23bp
Analyse The glucocorticoid receptor in complex with velsecorat, a PGC1a coactivator… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7PRW
- Type
- protein + DNA
- Length
- 705 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.502
- Source
- Homo sapiens; SYNTHETIC CONSTRUCT
- Molecule
- Glucocorticoid receptor; DNA (5'-D(*TP*CP*GP*AP*CP*GP*GP*AP*CP*AP*AP*AP*AP*TP*GP*TP*TP*CP*…
- UniProt
- P04150, Q9UBK2
- Ligands
- 82H, ZN
- Pockets
- 8 · best druggability 0.85
Structure
x-ray diffraction · resolution 2.502 · 5 distinct chains · 57% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glucocorticoid receptor | protein | 326 | 56% helix, 6% strand | P04150 |
| B | Glucocorticoid receptor | protein | 323 | 57% helix, 7% strand | P04150 |
| C | DNA (5'-D(*TP*CP*GP*AP*CP*GP*GP*AP*CP*AP*AP*AP*AP*TP*GP*TP*TP*CP*TP*GP*TP*AP*C)-3') | dna | 23 | — | — |
| D | DNA (5'-D(*GP*TP*AP*CP*AP*GP*AP*AP*CP*AP*TP*TP*TP*TP*GP*TP*CP*CP*GP*TP*CP*GP*A)-3') | dna | 23 | — | — |
| F | Peroxisome proliferator-activated receptor gamma coactivator 1-alpha | protein | 10 | 70% helix, 0% strand | Q9UBK2 |
Ligands and binding sites
- 82H · Velsecorat · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 4 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 6 copies · chains A, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 338 | 0.85 | 0.94 | 46 | 82H |
| 2 | 541 | 0.80 | 0.86 | 67 | 82H |
| 3 | 761 | 0.74 | 0.79 | 67 | empty |
| 4 | 563 | 0.70 | 0.79 | 39 | empty |
| 5 | 322 | 0.66 | 0.81 | 46 | EDO |
Interfaces
7 interfaces between chains.
- A–B · 1888 Ų buried · 25 hydrogen bonds · protein-protein
- C–D · 1036 Ų buried · 112 hydrogen bonds · nucleic-nucleic
- A–F · 522 Ų buried · 6 hydrogen bonds · protein-protein
- B–D · 381 Ų buried · 5 hydrogen bonds · protein-nucleic
- A–D · 371 Ų buried · 11 hydrogen bonds · protein-nucleic
Compared structures
- P04150 · AlphaFold monomer V2.0 prediction for glucocorticoid receptor (P04150) · a predicted model of the same protein · chain A against A, TM-score 0.78
- Q9UBK2 · AlphaFold monomer V2.0 prediction for peroxisome proliferator- activated receptor gamma… · a predicted model of the same protein · chain F against A, TM-score 0.70
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 Q9UBK2
- Elsewhere: RCSB PDB 7PRW · PDBe 7PRW · UniProt P04150 · UniProt Q9UBK2
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