MolNFT v1 · #41163 · protein
Estrogen receptor alpha lbd in complex with a tamoxifen-specific peptide antagonist
2JF9: “Estrogen receptor alpha lbd in complex with a tamoxifen-specific peptide antagonist”. X-ray diffraction, 3 ligands (OHT, BCT, CA), 10 pockets (best druggability 0.78). MolNFT v1 #41163 on GenesisL1: 3D structure, binding sites and…
- PDB
- 2JF9
- Type
- protein
- Length
- 677 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Estrogen receptor; AB5 peptide
- UniProt
- P03372
- Ligands
- OHT, BCT, CA
- Pockets
- 10 · best druggability 0.78
Structure
x-ray diffraction · 4 distinct chains · 72% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Estrogen receptor | protein | 215 | 72% helix, 4% strand | P03372 |
| B | Estrogen receptor | protein | 209 | 74% helix, 4% strand | P03372 |
| C | Estrogen receptor | protein | 214 | 70% helix, 4% strand | P03372 |
| P, Q, R | AB5 peptide | protein | 13 | 62% helix, 0% strand | — |
Ligands and binding sites
- OHT · 4-hydroxytamoxifen · ligand · 3 copies · chains A, P, B, Q, C, R
- BCT · Bicarbonate ion · ligand · chains A, C
- CA · Calcium ion · metal · 2 copies · chains C, P, A, R
- EDO · 1,2-ethanediol · additive · 6 copies · chains A, C, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 226 | 0.78 | 0.91 | 27 | OHT |
| 2 | 218 | 0.77 | 0.91 | 28 | OHT |
| 3 | 227 | 0.77 | 0.90 | 29 | OHT |
| 4 | 119 | 0.67 | 0.89 | 19 | empty |
| 5 | 102 | 0.66 | 0.90 | 20 | empty |
Interfaces
7 interfaces between chains.
- A–B · 1644 Ų buried · 28 hydrogen bonds · protein-protein
- C–R · 552 Ų buried · 2 hydrogen bonds · protein-protein
- B–Q · 552 Ų buried · 2 hydrogen bonds · protein-protein
- A–P · 539 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 459 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 2JF9 · Estrogen receptor alpha lbd in complex with a tamoxifen-specific peptide antagonist · the same entry in another collection · chain R against R, TM-score 1.00
- P03372 · AlphaFold monomer V2.0 prediction for estrogen receptor (P03372) · a predicted model of the same protein · chain A 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 P03372
- Elsewhere: RCSB PDB 2JF9 · PDBe 2JF9 · UniProt P03372
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.