MolNFT v1 · #190684 · protein
Human estrogen receptor beta ligand-binding domain in complex with S- dpn
7XVY: “Human estrogen receptor beta ligand-binding domain in complex with S- dpn”. X-ray diffraction, 1 ligand (I0K), 7 pockets (best druggability 0.83). MolNFT v1 #190684 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7XVY
- Type
- protein
- Length
- 463 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Estrogen receptor beta; Nuclear receptor coactivator 1
- EC
- 2.3.1.48
- UniProt
- Q92731, Q15788
- Ligands
- I0K
- Pockets
- 7 · best druggability 0.83
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 | 73% helix, 3% strand | Q92731 |
| B | Estrogen receptor beta | protein | 224 | 71% helix, 4% strand | Q92731 |
| C | Nuclear receptor coactivator 1 (EC 2.3.1.48) | protein | 11 | 64% helix, 0% strand | Q15788 |
| D | Nuclear receptor coactivator 1 (EC 2.3.1.48) | protein | 10 | 70% helix, 0% strand | Q15788 |
Ligands and binding sites
- I0K · (2~{S})-2,3-bis(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
7 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 | 23 | I0K |
| 2 | 150 | 0.82 | 0.97 | 21 | I0K |
| 3 | 101 | 0.78 | 0.97 | 28 | empty |
| 4 | 558 | 0.65 | 0.76 | 53 | empty |
| 5 | 139 | 0.61 | 0.85 | 21 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1096 Ų buried · 13 hydrogen bonds · protein-protein
- A–C · 463 Ų buried · 8 hydrogen bonds · protein-protein
- B–D · 447 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 7XVY · Human Estrogen Receptor beta Ligand-binding Domain in Complex with S-DPN · 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 0.98
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
- Every structure of UniProt Q15788
- Elsewhere: RCSB PDB 7XVY · PDBe 7XVY · UniProt Q92731 · UniProt Q15788
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