MolNFT v1 · #117062 · protein
Estrogen receptor alpha ligand binding domain Y537S mutant in complex with stapled peptide SRC2-P3 and estradiol
5DX3: “Estrogen receptor alpha ligand binding domain Y537S mutant in complex with stapled peptide SRC2-P3 and…”. X-ray diffraction, 4 ligands (ACE, EST, NH2), 6 pockets (best druggability 0.84). MolNFT v1 #117062 on GenesisL1: 3D…
- PDB
- 5DX3
- Type
- protein
- Length
- 477 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Estrogen receptor; Stapled peptide SRC2-P3
- UniProt
- P03372, Q15596
- Ligands
- ACE, EST, NH2, CL
- Pockets
- 6 · best druggability 0.84
Structure
x-ray diffraction · 3 distinct chains · 70% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Estrogen receptor | protein | 231 | 69% helix, 4% strand | P03372 |
| B | Estrogen receptor | protein | 224 | 71% helix, 4% strand | P03372 |
| C, D | Stapled peptide SRC2-P3 | protein | 11 | 45% helix, 0% strand | Q15596 |
Ligands and binding sites
- ACE · Acetyl group · ligand · 2 copies · chains C, D
- EST · Estradiol · ligand · 2 copies · chains A, B
- NH2 · Amino group · ion · 2 copies · chains C, D
- CL · Chloride ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 176 | 0.84 | 0.98 | 22 | EST |
| 2 | 192 | 0.84 | 0.97 | 21 | EST |
| 3 | 479 | 0.66 | 0.78 | 49 | empty |
| 4 | 79 | 0.65 | 0.92 | 17 | empty |
| 5 | 214 | 0.63 | 0.83 | 30 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1522 Ų buried · 16 hydrogen bonds · protein-protein
- A–C · 542 Ų buried · 3 hydrogen bonds · protein-protein
- B–D · 468 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified, 2 covalent (nonstandard, covalent ligand).
Compared structures
- 5DX3 · Estrogen Receptor Alpha Ligand Binding Domain Y537S Mutant in Complex with Stapled… · 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 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 P03372
- Every structure of UniProt Q15596
- Elsewhere: RCSB PDB 5DX3 · PDBe 5DX3 · UniProt P03372 · UniProt Q15596
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