Research workbench
Crystal structure of the er-alpha ligand-binding domain (Y537S) in complex with an N-methyl, 2-chlorobenzyl obhs-N derivative
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
- 5KCE
- Type
- protein
- Length
- 480 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
- OB3
- Pockets
- 7 · best druggability 0.85
Structure
x-ray diffraction · 4 distinct chains · 68% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Estrogen receptor | protein | 223 | 70% helix, 4% strand | P03372 |
| B | Estrogen receptor | protein | 239 | 67% helix, 4% strand | P03372 |
| C | Nuclear receptor coactivator 2 | protein | 10 | 60% helix, 0% strand | Q15596 |
| D | Nuclear receptor coactivator 2 | protein | 8 | 63% helix, 0% strand | Q15596 |
Ligands and binding sites
- OB3 · (1S,2R,4S)-N-(2-chlorophenyl)-5,6-bis(4-hydroxyphenyl)-N-methyl-7-oxabicyclo[2.2.1]hept-5-ene-2-sulfonamide · ligand · 3 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, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 269 | 0.85 | 0.95 | 27 | OB3 |
| 2 | 307 | 0.82 | 0.92 | 30 | OB3 |
| 3 | 90 | 0.67 | 0.92 | 17 | empty |
| 4 | 400 | 0.65 | 0.79 | 46 | empty |
| 5 | 80 | 0.63 | 0.90 | 17 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1753 Ų buried · 31 hydrogen bonds · protein-protein
- A–D · 490 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 490 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 5KCE · Crystal Structure of the ER-alpha Ligand-binding Domain (Y537S) in Complex with an… · 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 0.98
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 5KCE · PDBe 5KCE · UniProt P03372 · UniProt Q15596
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