Research workbench
Progesterone receptor ligand binding domain with bound norethindrone
Analyse Progesterone receptor ligand binding domain with bound norethindrone in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1SQN
- Type
- protein
- Length
- 498 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Progesterone receptor
- UniProt
- P06401
- Ligands
- NDR
- Pockets
- 12 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 69% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Progesterone receptor | protein | 248 | 70% helix, 4% strand | P06401 |
| B | Progesterone receptor | protein | 250 | 68% helix, 4% strand | P06401 |
Ligands and binding sites
- NDR · (14beta,17alpha)-17-ethynyl-17-hydroxyestr-4-en-3-one · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 197 | 0.85 | 0.98 | 23 | NDR |
| 2 | 196 | 0.84 | 0.97 | 23 | NDR |
| 3 | 187 | 0.66 | 0.85 | 25 | empty |
| 4 | 193 | 0.66 | 0.85 | 24 | empty |
| 5 | 111 | 0.57 | 0.84 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 566 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 1SQN · Progesterone Receptor Ligand Binding Domain with bound Norethindrone · the same entry in another collection · chain A against A, TM-score 1.00
- P06401 · AlphaFold monomer V2.0 prediction for progesterone receptor (P06401) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 P06401
- Elsewhere: RCSB PDB 1SQN · PDBe 1SQN · UniProt P06401
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