Research workbench
Estrogen receptor alpha ligand binding domain in complex with the selective estrogen receptor modulator clomiphene
Analyse Estrogen receptor alpha ligand binding domain in complex with the selective… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6VPF
- Type
- protein
- Length
- 952 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Estrogen receptor
- UniProt
- P03372
- Ligands
- 53Q
- Pockets
- 14 · best druggability 0.85
Structure
x-ray diffraction · 4 distinct chains · 69% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Estrogen receptor | protein | 243 | 68% helix, 4% strand | P03372 |
| A | Estrogen receptor | protein | 236 | 69% helix, 4% strand | P03372 |
| C | Estrogen receptor | protein | 237 | 70% helix, 4% strand | P03372 |
| D | Estrogen receptor | protein | 236 | 68% helix, 4% strand | P03372 |
Ligands and binding sites
- 53Q · Clomifene · ligand · 4 copies · chains B, A, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 997 | 0.85 | 0.85 | 112 | 53Q |
| 2 | 237 | 0.81 | 0.93 | 31 | 53Q |
| 3 | 232 | 0.81 | 0.93 | 30 | 53Q |
| 4 | 89 | 0.59 | 0.87 | 18 | empty |
| 5 | 119 | 0.58 | 0.84 | 21 | empty |
Interfaces
4 interfaces between chains.
- B–D · 1581 Ų buried · 25 hydrogen bonds · protein-protein
- A–C · 603 Ų buried · 6 hydrogen bonds · protein-protein
- B–A · 499 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 243 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 6VPF · Estrogen Receptor Alpha Ligand Binding Domain in Complex with the Selective Estrogen… · the same entry in another collection · chain D against D, 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 0.92
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 6VPF · PDBe 6VPF · UniProt P03372
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