MolNFT v1 · #135551 · protein
Crystal structure of the er-alpha ligand-binding domain (Y537S) in complex with oxabicyclic heptene sulfonate (obhs)
5U2D · Estrogen receptor: “Crystal structure of the er-alpha ligand-binding domain (Y537S) in complex with oxabicyclic heptene sulfonate…”. X-ray diffraction, 1 ligand (OBH), 8 pockets (best druggability 0.84). MolNFT v1 #135551 on…
- PDB
- 5U2D
- Type
- protein
- Length
- 508 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
- OBH
- Pockets
- 8 · best druggability 0.84
Structure
x-ray diffraction · 4 distinct chains · 69% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Estrogen receptor | protein | 246 | 70% helix, 4% strand | P03372 |
| B | Estrogen receptor | protein | 239 | 69% helix, 3% strand | P03372 |
| C | Nuclear receptor coactivator 2 | protein | 12 | 58% helix, 0% strand | Q15596 |
| D | Nuclear receptor coactivator 2 | protein | 11 | 55% helix, 0% strand | Q15596 |
Ligands and binding sites
- OBH · cyclohexa-2,5-dien-1-yl (1S,2R,4S)-5,6-bis(4-hydroxyphenyl)-7-oxabicyclo[2.2.1]hept-5-ene-2-sulfonate · ligand · 2 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, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 225 | 0.84 | 0.97 | 30 | OBH |
| 2 | 221 | 0.83 | 0.96 | 29 | OBH |
| 3 | 86 | 0.67 | 0.92 | 17 | empty |
| 4 | 95 | 0.63 | 0.89 | 19 | empty |
| 5 | 253 | 0.57 | 0.78 | 33 | empty |
Interfaces
3 interfaces between chains.
- A–B · 2127 Ų buried · 37 hydrogen bonds · protein-protein
- A–C · 563 Ų buried · 5 hydrogen bonds · protein-protein
- B–D · 527 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 5U2D · 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 0.97
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 5U2D · PDBe 5U2D · UniProt P03372 · UniProt Q15596
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