MolNFT v1 · #116981 · protein
Crystal structure of the er-alpha ligand-binding domain in complex with a sulfoxide-bridged oxabicyclic heptene sulfonate (sobhs)-3 analog phenyl (1S,2S,4S,7S)-5,6-BIS(4-hydroxy-3-methylphenyl)-7- THIABICYCLO[2.2.1]HEPT-5-ene-2-sulfonate 7-oxide
5DUH · Estrogen receptor: “Crystal structure of the er-alpha ligand-binding domain in complex with a sulfoxide-bridged oxabicyclic…”. X-ray diffraction, 1 ligand (5FT), 8 pockets (best druggability 0.85). MolNFT v1 #116981 on GenesisL1: 3D…
- PDB
- 5DUH
- Type
- protein
- Length
- 488 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
- 5FT
- Pockets
- 8 · best druggability 0.85
Structure
x-ray diffraction · 4 distinct chains · 70% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Estrogen receptor | protein | 236 | 70% helix, 4% strand | P03372 |
| B | Estrogen receptor | protein | 233 | 70% helix, 4% strand | P03372 |
| C | Nuclear receptor coactivator 2 | protein | 10 | 50% helix, 0% strand | Q15596 |
| D | Nuclear receptor coactivator 2 | protein | 9 | 78% helix, 0% strand | Q15596 |
Ligands and binding sites
- 5FT · phenyl (1S,2S,4S,7S)-5,6-bis(4-hydroxy-3-methylphenyl)-7-thiabicyclo[2.2.1]hept-5-ene-2-sulfonate 7-oxide · 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 | 246 | 0.85 | 0.97 | 30 | 5FT |
| 2 | 262 | 0.84 | 0.95 | 29 | 5FT |
| 3 | 113 | 0.66 | 0.89 | 19 | empty |
| 4 | 121 | 0.65 | 0.88 | 21 | empty |
| 5 | 100 | 0.56 | 0.85 | 25 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1722 Ų buried · 25 hydrogen bonds · protein-protein
- B–D · 521 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 507 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 5DUH · Crystal Structure of the ER-alpha Ligand-binding Domain in Complex with a… · 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 5DUH · PDBe 5DUH · UniProt P03372 · UniProt Q15596
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