Research workbench
Estrogen receptor alpha ligand binding domain Y537S mutant in complex with SRC2 stapled peptide 41A and estradiol
Analyse Estrogen receptor alpha ligand binding domain Y537S mutant in complex with SRC2… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6PIT
- Type
- protein
- Length
- 448 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Estrogen receptor; Stapled peptide 41A
- UniProt
- P03372
- Ligands
- LOU, EST
- Pockets
- 7 · 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 | 221 | 71% helix, 4% strand | P03372 |
| B | Estrogen receptor | protein | 218 | 68% helix, 4% strand | P03372 |
| D | Stapled peptide 41A | protein | 7 | 0% helix, 0% strand | — |
| C | Stapled peptide 41A | protein | 2 | 0% helix, 0% strand | — |
Ligands and binding sites
- LOU · 3-[(3ar,4s,7s,7as)-2-(carboxymethyl)-1,3-dioxooctahydro-4H-4,7-epoxyisoindol-4-yl]-L-alanine · ligand · 2 copies · chains B, D, A, C
- EST · Estradiol · 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 | 182 | 0.84 | 0.98 | 23 | EST |
| 2 | 174 | 0.84 | 0.97 | 22 | EST |
| 3 | 105 | 0.63 | 0.88 | 21 | empty |
| 4 | 91 | 0.59 | 0.87 | 20 | empty |
| 5 | 184 | 0.52 | 0.78 | 27 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1666 Ų buried · 24 hydrogen bonds · protein-protein
- B–D · 403 Ų buried · 1 hydrogen bond · protein-protein
- A–C · 149 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 covalent, 2 modified (covalent ligand, methylation).
Compared structures
- 6PIT · Estrogen Receptor Alpha Ligand Binding Domain Y537S Mutant in Complex with SRC2 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
- Elsewhere: RCSB PDB 6PIT · PDBe 6PIT · UniProt P03372
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