Research workbench
Crystal structure of the human progesterone receptor ligand- binding domain bound to levonorgestrel
Analyse Crystal structure of the human progesterone receptor ligand- binding domain… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3D90
- Type
- protein
- Length
- 496 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Progesterone receptor
- UniProt
- P06401
- Ligands
- NOG
- Pockets
- 10 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 67% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Progesterone receptor | protein | 247 | 66% helix, 4% strand | P06401 |
| B | Progesterone receptor | protein | 249 | 67% helix, 4% strand | P06401 |
Ligands and binding sites
- NOG · 13-beta-ethyl-17-alpha-ethynyl-17-beta-hydroxygon-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
10 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 230 | 0.86 | 0.98 | 25 | NOG |
| 2 | 222 | 0.85 | 0.97 | 24 | NOG |
| 3 | 208 | 0.71 | 0.87 | 24 | empty |
| 4 | 234 | 0.69 | 0.85 | 24 | empty |
| 5 | 125 | 0.64 | 0.88 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 544 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 3D90 · Crystal structure of the human progesterone receptor ligand-binding domain bound to… · 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 3D90 · PDBe 3D90 · UniProt P06401
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