Research workbench
Crystal structure of the er-alpha ligand-binding domain (Y537S) in complex with 2,5-BIS(2-chloro-4-HYDROXYPHENYL)THIOPHENE 1-oxide
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
- 5TM2
- Type
- protein
- Length
- 466 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
- 7EO
- Pockets
- 7 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 69% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Estrogen receptor | protein | 217 | 71% helix, 3% strand | P03372 |
| B | Estrogen receptor | protein | 231 | 67% helix, 4% strand | P03372 |
| C, D | Nuclear receptor coactivator 2 | protein | 9 | 78% helix, 0% strand | Q15596 |
Ligands and binding sites
- 7EO · 2,5-bis(2-chloro-4-hydroxyphenyl)-1H-1lambda~4~-thiophen-1-one · 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, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 238 | 0.81 | 0.93 | 25 | 7EO |
| 2 | 498 | 0.80 | 0.87 | 39 | 7EO |
| 3 | 89 | 0.66 | 0.91 | 18 | empty |
| 4 | 103 | 0.64 | 0.89 | 21 | empty |
| 5 | 75 | 0.55 | 0.87 | 22 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1565 Ų buried · 23 hydrogen bonds · protein-protein
- B–D · 453 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 428 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 5TM2 · Crystal Structure of the ER-alpha Ligand-binding Domain (Y537S) in Complex with… · 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 A 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 5TM2 · PDBe 5TM2 · UniProt P03372 · UniProt Q15596
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