Research workbench
Human estrogen receptor beta ligand-binding domain in complex with (R)-3-(2-chloro-4-hydroxyphenyl)-2-(4-HYDROXYPHENYL)PROPANENITRILE
Analyse Human estrogen receptor beta ligand-binding domain in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7XVZ
- Type
- protein
- Length
- 462 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Estrogen receptor beta; Src peptide
- UniProt
- Q92731
- Ligands
- I1D
- Pockets
- 6 · best druggability 0.82
Structure
x-ray diffraction · 4 distinct chains · 72% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Estrogen receptor beta | protein | 218 | 72% helix, 3% strand | Q92731 |
| B | Estrogen receptor beta | protein | 224 | 71% helix, 4% strand | Q92731 |
| C | Src peptide | protein | 10 | 70% helix, 0% strand | — |
| D | Src peptide | protein | 10 | 70% helix, 0% strand | — |
Ligands and binding sites
- I1D · (2~{R})-3-(2-chloranyl-4-oxidanyl-phenyl)-2-(4-hydroxyphenyl)propanenitrile · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 159 | 0.82 | 0.97 | 22 | I1D |
| 2 | 164 | 0.82 | 0.97 | 21 | I1D |
| 3 | 990 | 0.77 | 0.79 | 88 | empty |
| 4 | 116 | 0.62 | 0.87 | 21 | empty |
| 5 | 98 | 0.55 | 0.84 | 20 | empty |
Interfaces
3 interfaces between chains.
- A–B · 950 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 437 Ų buried · 2 hydrogen bonds · protein-protein
- B–D · 425 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 7XVZ · Human Estrogen Receptor beta Ligand-binding Domain in Complex with… · the same entry in another collection · chain A against A, TM-score 1.00
- Q92731 · AlphaFold monomer V2.0 prediction for estrogen receptor beta (Q92731) · 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 Q92731
- Elsewhere: RCSB PDB 7XVZ · PDBe 7XVZ · UniProt Q92731
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