MolNFT v1 · #28790 · protein
Structure of the steroidogenic factor-1 ligand binding domain bound to phospholipid and a shp peptide motif
1YP0 · Nuclear receptor subfamily 5, group a, member 1: “Structure of the steroidogenic factor-1 ligand binding domain bound to phospholipid and a shp peptide motif”. X-ray diffraction, 1 ligand (PEF), 3 pockets (best druggability 0.84).…
- PDB
- 1YP0
- Type
- protein
- Length
- 251 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nuclear receptor subfamily 5, group a, member 1; Nuclear receptor subfamily 0, group B…
- UniProt
- P33242, P97947
- Ligands
- PEF
- Pockets
- 3 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 70% helix, 2% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nuclear receptor subfamily 5, group a, member 1 | protein | 239 | 71% helix, 3% strand | P33242 |
| B | Nuclear receptor subfamily 0, group B, member 2 | protein | 12 | 50% helix, 0% strand | P97947 |
Ligands and binding sites
- PEF · Di-palmitoyl-3-sn-phosphatidylethanolamine · ligand · 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 | 618 | 0.84 | 0.88 | 48 | PEF |
| 2 | 114 | 0.65 | 0.89 | 22 | empty |
| 3 | 81 | 0.38 | 0.77 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 513 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 1YP0 · Structure of the steroidogenic factor-1 ligand binding domain bound to phospholipid and a… · the same entry in another collection · chain A against A, TM-score 1.00
- P33242 · AlphaFold monomer V2.0 prediction for steroidogenic factor 1 (P33242) · a predicted model of the same protein · chain A against A, TM-score 0.93
- P97947 · AlphaFold monomer V2.0 prediction for nuclear receptor subfamily 0 group B member 2… · a predicted model of the same protein · chain B against A, TM-score 0.59
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 P33242
- Every structure of UniProt P97947
- Elsewhere: RCSB PDB 1YP0 · PDBe 1YP0 · UniProt P33242 · UniProt P97947
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