MolNFT v1 · #117070 · protein
Estrogen receptor alpha ligand binding domain Y537S mutant in complex with stapled peptide SRC2-P1 and estradiol
5DXB: “Estrogen receptor alpha ligand binding domain Y537S mutant in complex with stapled peptide SRC2-P1 and…”. X-ray diffraction, 4 ligands (EST, ACE, NH2), 5 pockets (best druggability 0.84). MolNFT v1 #117070 on GenesisL1: 3D…
- PDB
- 5DXB
- Type
- protein
- Length
- 476 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Estrogen receptor; Nuclear receptor coactivator 2
- UniProt
- P03372, Q15596
- Ligands
- EST, ACE, NH2, CL
- Pockets
- 5 · best druggability 0.84
Structure
x-ray diffraction · 4 distinct chains · 68% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Estrogen receptor | protein | 232 | 69% helix, 4% strand | P03372 |
| B | Estrogen receptor | protein | 224 | 69% helix, 4% strand | P03372 |
| D | Nuclear receptor coactivator 2 | protein | 11 | 45% helix, 0% strand | Q15596 |
| E | Nuclear receptor coactivator 2 | protein | 9 | 56% helix, 0% strand | Q15596 |
Ligands and binding sites
- EST · Estradiol · ligand · 2 copies · chains A, B
- ACE · Acetyl group · ligand · chains D
- NH2 · Amino group · ion · chains D
- CL · Chloride ion · ion · chains B
- GOL · Glycerol · additive · 2 copies · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 189 | 0.84 | 0.98 | 23 | EST |
| 2 | 177 | 0.84 | 0.98 | 21 | EST |
| 3 | 606 | 0.69 | 0.78 | 57 | empty |
| 4 | 96 | 0.62 | 0.88 | 21 | empty |
| 5 | 81 | 0.60 | 0.89 | 18 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1591 Ų buried · 23 hydrogen bonds · protein-protein
- A–D · 539 Ų buried · 5 hydrogen bonds · protein-protein
- B–E · 493 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 modified, 1 covalent (nonstandard, covalent ligand, methylation).
Compared structures
- 5DXB · Estrogen Receptor Alpha Ligand Binding Domain Y537S Mutant in Complex with Stapled… · the same entry in another collection · chain E against E, 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 5DXB · PDBe 5DXB · UniProt P03372 · UniProt Q15596
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