Research workbench
Crystal structure of the er-alpha ligand-binding domain (Y537S) in complex with the obhs-asc analog, 5-(4-((1R,4S,6R)-6-((3- CHLOROPHENOXY)SULFONYL)-3-(4-hydroxyphenyl)-7-OXABICYCLO[2.2.1]HEPT- 2-en-2-YL)PHENOXY)PENTANOIC acid
Analyse Crystal structure of the er-alpha ligand-binding domain (Y537S) in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5TM4
- Type
- protein
- Length
- 463 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
- 7E3
- Pockets
- 8 · best druggability 0.80
Structure
x-ray diffraction · 4 distinct chains · 68% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Estrogen receptor | protein | 228 | 66% helix, 4% strand | P03372 |
| B | Estrogen receptor | protein | 218 | 70% helix, 4% strand | P03372 |
| C | Nuclear receptor coactivator 2 | protein | 9 | 78% helix, 0% strand | Q15596 |
| D | Nuclear receptor coactivator 2 | protein | 8 | 75% helix, 0% strand | Q15596 |
Ligands and binding sites
- 7E3 · 5-{4-[(1S,4S,6R)-6-[(3-chlorophenoxy)sulfonyl]-3-(4-hydroxyphenyl)-7-oxabicyclo[2.2.1]hept-2-en-2-yl]phenoxy}pentanoic acid · ligand · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 324 | 0.80 | 0.89 | 31 | 7E3 |
| 2 | 298 | 0.78 | 0.89 | 29 | 7E3 |
| 3 | 94 | 0.64 | 0.89 | 17 | empty |
| 4 | 94 | 0.64 | 0.89 | 17 | empty |
| 5 | 78 | 0.52 | 0.85 | 19 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1725 Ų buried · 29 hydrogen bonds · protein-protein
- B–D · 488 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 466 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 5TM4 · Crystal Structure of the ER-alpha Ligand-binding Domain (Y537S) in Complex with the… · 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 5TM4 · PDBe 5TM4 · UniProt P03372 · UniProt Q15596
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