MolNFT v1 · #32200 · protein
Estrogen receptor alpha lbd in complex with a phage-display derived peptide antagonist
2BJ4: “Estrogen receptor alpha lbd in complex with a phage-display derived peptide antagonist”. X-ray diffraction, 1 ligand (OHT), 8 pockets (best druggability 0.79). MolNFT v1 #32200 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 2BJ4
- Type
- protein
- Length
- 462 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Estrogen receptor; Peptide antagonist
- UniProt
- P03372
- Ligands
- OHT
- Pockets
- 8 · best druggability 0.79
Structure
x-ray diffraction · 3 distinct chains · 72% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Estrogen receptor | protein | 218 | 74% helix, 5% strand | P03372 |
| B | Estrogen receptor | protein | 222 | 71% helix, 5% strand | P03372 |
| C, D | Peptide antagonist | protein | 11 | 27% helix, 9% strand | — |
Ligands and binding sites
- OHT · 4-hydroxytamoxifen · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 199 | 0.79 | 0.93 | 25 | OHT |
| 2 | 190 | 0.79 | 0.93 | 23 | OHT |
| 3 | 81 | 0.76 | 0.98 | 19 | empty |
| 4 | 68 | 0.72 | 0.97 | 17 | empty |
| 5 | 138 | 0.45 | 0.77 | 21 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1561 Ų buried · 25 hydrogen bonds · protein-protein
- B–D · 727 Ų buried · 15 hydrogen bonds · protein-protein
- A–C · 699 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (nonstandard).
Compared structures
- 2BJ4 · Estrogen receptor alpha lbd in complex with a phage-display derived peptide antagonist · the same entry in another collection · chain A against A, 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 0.98
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 P03372
- Elsewhere: RCSB PDB 2BJ4 · PDBe 2BJ4 · UniProt P03372
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