MolNFT v1 · #160384 · protein
Estrogen receptor alpha ligand binding domain Y537S mutant in complex with SRC2 stapled peptide 41A and estradiol
6PIT: “Estrogen receptor alpha ligand binding domain Y537S mutant in complex with SRC2 stapled peptide 41A and…”. X-ray diffraction, 2 ligands (LOU, EST), 7 pockets (best druggability 0.84). MolNFT v1 #160384 on GenesisL1: 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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