Research workbench
Stapled peptide bound to estrogen receptor beta
Analyse Stapled peptide bound to estrogen receptor beta in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2YJD
- Type
- protein
- Length
- 468 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Estrogen receptor beta; Stapled peptide
- UniProt
- Q92731
- Ligands
- ACE, YJD, NH2
- Pockets
- 6 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 71% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Estrogen receptor beta | protein | 223 | 71% helix, 4% strand | Q92731 |
| C, D | Stapled peptide | protein | 11 | 64% helix, 0% strand | — |
Ligands and binding sites
- ACE · Acetyl group · ligand · 2 copies · chains A, C, B, D
- YJD · 4-(2-propan-2-yloxybenzimidazol-1-yl)phenol · ligand · 2 copies · chains A, B
- NH2 · Amino group · ion · 2 copies · chains C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 149 | 0.83 | 0.98 | 22 | YJD |
| 2 | 154 | 0.83 | 0.98 | 22 | YJD |
| 3 | 93 | 0.65 | 0.90 | 19 | empty |
| 4 | 132 | 0.61 | 0.85 | 23 | empty |
| 5 | 351 | 0.61 | 0.78 | 39 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1200 Ų buried · 18 hydrogen bonds · protein-protein
- B–D · 462 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 459 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified, 2 covalent (nonstandard, covalent ligand).
Compared structures
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 Q92731
- Elsewhere: RCSB PDB 2YJD · PDBe 2YJD · UniProt Q92731
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