Research workbench
Crystal structure of the er-alpha ligand-binding domain (Y537S) in complex with an N-trifluoroethyl 4-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
- 5KD9
- Type
- protein
- Length
- 482 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Estrogen receptor; NCOA2
- UniProt
- P03372
- Ligands
- OBT
- Pockets
- 6 · best druggability 0.84
Structure
x-ray diffraction · 4 distinct chains · 68% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Estrogen receptor | protein | 235 | 70% helix, 3% strand | P03372 |
| B | Estrogen receptor | protein | 228 | 67% helix, 3% strand | P03372 |
| C | NCOA2 | protein | 10 | 70% helix, 0% strand | — |
| D | NCOA2 | protein | 9 | 78% helix, 0% strand | — |
Ligands and binding sites
- OBT · (1S,2R,4S)-N-(4-chlorophenyl)-5,6-bis(4-hydroxyphenyl)-N-(2,2,2-trifluoroethyl)-7-oxabicyclo[2.2.1]hept-5-ene-2-sulfonamide · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 209 | 0.84 | 0.96 | 29 | OBT |
| 2 | 344 | 0.83 | 0.91 | 30 | OBT |
| 3 | 98 | 0.67 | 0.91 | 20 | empty |
| 4 | 100 | 0.66 | 0.90 | 18 | empty |
| 5 | 130 | 0.43 | 0.76 | 21 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1669 Ų buried · 22 hydrogen bonds · protein-protein
- A–C · 505 Ų buried · 3 hydrogen bonds · protein-protein
- B–D · 484 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 5KD9 · 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
- Elsewhere: RCSB PDB 5KD9 · PDBe 5KD9 · UniProt P03372
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