MolNFT v1 · #46131 · protein
Crystal structure of estrogen receptor beta complexed with way-555
2NV7: “Crystal structure of estrogen receptor beta complexed with way-555”. X-ray diffraction, 1 ligand (555), 7 pockets (best druggability 0.83). MolNFT v1 #46131 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2NV7
- Type
- protein
- Length
- 473 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
- 555
- Pockets
- 7 · best druggability 0.83
Structure
x-ray diffraction · 3 distinct chains · 71% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Estrogen receptor beta | protein | 228 | 71% helix, 3% strand | Q92731 |
| B | Estrogen receptor beta | protein | 225 | 71% helix, 4% strand | Q92731 |
| C, D | Nuclear receptor coactivator 1 (EC 2.3.1.48) | protein | 10 | 70% helix, 0% strand | Q15788 |
Ligands and binding sites
- 555 · 4-(4-hydroxyphenyl)-1-naphthaldehyde oxime · 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, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 157 | 0.83 | 0.98 | 23 | 555 |
| 2 | 154 | 0.82 | 0.97 | 23 | 555 |
| 3 | 78 | 0.68 | 0.93 | 18 | empty |
| 4 | 467 | 0.63 | 0.77 | 43 | empty |
| 5 | 124 | 0.61 | 0.86 | 22 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1248 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 478 Ų buried · 8 hydrogen bonds · protein-protein
- B–D · 446 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 2NV7 · Crystal Structure of Estrogen Receptor Beta Complexed with WAY-555 · 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
- Every structure of UniProt Q15788
- Elsewhere: RCSB PDB 2NV7 · PDBe 2NV7 · UniProt Q92731 · UniProt Q15788
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