Research workbench
Crystal structure of the er-alpha ligand-binding domain (Y537S) in complex with 16-benzylidene estrone
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
- 5KRH
- Type
- protein
- Length
- 488 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Estrogen receptor; NCOA2
- UniProt
- P03372
- Ligands
- 6WN
- Pockets
- 6 · best druggability 0.79
Structure
x-ray diffraction · 3 distinct chains · 69% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Estrogen receptor | protein | 231 | 68% helix, 4% strand | P03372 |
| B | Estrogen receptor | protein | 237 | 69% helix, 3% strand | P03372 |
| C, D | NCOA2 | protein | 10 | 70% helix, 0% strand | — |
Ligands and binding sites
- 6WN · (8~{R},9~{S},13~{S},14~{S},16~{E})-13-methyl-3-oxidanyl-16-(phenylmethylidene)-6,7,8,9,11,12,14,15-octahydrocyclopenta[a]phenanthren-17-one · 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 | 365 | 0.79 | 0.88 | 48 | 6WN |
| 2 | 434 | 0.76 | 0.85 | 47 | 6WN |
| 3 | 96 | 0.63 | 0.89 | 19 | empty |
| 4 | 85 | 0.62 | 0.89 | 18 | empty |
| 5 | 145 | 0.42 | 0.75 | 24 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1653 Ų buried · 24 hydrogen bonds · protein-protein
- A–C · 539 Ų buried · 2 hydrogen bonds · protein-protein
- B–D · 491 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 5KRH · 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 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 5KRH · PDBe 5KRH · UniProt P03372
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