Research workbench
Crystal structure of the er-alpha ligand-binding domain (Y537S) in complex with the dynamic way derivative, 1A
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
- 5KRF
- Type
- protein
- Length
- 490 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Estrogen receptor; Khkilhrllqdsss peptide
- UniProt
- P03372
- Ligands
- 6WL
- Pockets
- 9 · best druggability 0.84
Structure
x-ray diffraction · 3 distinct chains · 67% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Estrogen receptor | protein | 234 | 69% helix, 3% strand | P03372 |
| B | Estrogen receptor | protein | 236 | 67% helix, 4% strand | P03372 |
| C, D | Khkilhrllqdsss peptide | protein | 10 | 50% helix, 0% strand | — |
Ligands and binding sites
- 6WL · 4-[1-methyl-7-(trifluoromethyl)indazol-3-yl]benzene-1, 3-diol · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 170 | 0.84 | 0.98 | 23 | 6WL |
| 2 | 189 | 0.83 | 0.96 | 22 | 6WL |
| 3 | 75 | 0.63 | 0.91 | 16 | empty |
| 4 | 82 | 0.63 | 0.90 | 16 | empty |
| 5 | 256 | 0.60 | 0.80 | 35 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1669 Ų buried · 34 hydrogen bonds · protein-protein
- A–C · 535 Ų buried · 4 hydrogen bonds · protein-protein
- B–D · 528 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 5KRF · Crystal Structure of the ER-alpha Ligand-binding Domain (Y537S) in Complex with the… · 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 0.98
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 5KRF · PDBe 5KRF · UniProt P03372
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