Research workbench
Crystal structure of the er-alpha ligand-binding domain (Y537S) in complex with a squaric acid-linked dimeric estrogen
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
- 5TLO
- Type
- protein
- Length
- 479 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Estrogen receptor; Nuclear receptor coactivator 2
- UniProt
- P03372
- Ligands
- 7EE
- Pockets
- 7 · best druggability 0.82
Structure
x-ray diffraction · 3 distinct chains · 68% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Estrogen receptor | protein | 229 | 69% helix, 4% strand | P03372 |
| B | Estrogen receptor | protein | 232 | 68% helix, 4% strand | P03372 |
| C, D | Nuclear receptor coactivator 2 | protein | 9 | 78% helix, 0% strand | — |
Ligands and binding sites
- 7EE · (14beta,17alpha)-21-(4-aminophenyl)-19-norpregna-1(10), 2,4-trien-20-yne-3,17-diol · 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 | 297 | 0.82 | 0.91 | 31 | 7EE |
| 2 | 299 | 0.81 | 0.91 | 32 | 7EE |
| 3 | 85 | 0.64 | 0.90 | 19 | empty |
| 4 | 80 | 0.63 | 0.90 | 17 | empty |
| 5 | 184 | 0.53 | 0.79 | 26 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1613 Ų buried · 23 hydrogen bonds · protein-protein
- B–D · 516 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 503 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 5TLO · Crystal Structure of the ER-alpha Ligand-binding Domain (Y537S) in Complex with a Squaric… · 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 5TLO · PDBe 5TLO · UniProt P03372
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