Research workbench
Crystal structure of the er-alpha ligand-binding domain (Y537S) in complex with zearalenone
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
- 5KRC
- Type
- protein
- Length
- 491 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Estrogen receptor; NCOA2
- UniProt
- P03372
- Ligands
- ZER
- Pockets
- 7 · best druggability 0.86
Structure
x-ray diffraction · 3 distinct chains · 65% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Estrogen receptor | protein | 233 | 67% helix, 4% strand | P03372 |
| B | Estrogen receptor | protein | 238 | 65% helix, 3% strand | P03372 |
| C, D | NCOA2 | protein | 10 | 50% helix, 0% strand | — |
Ligands and binding sites
- ZER · (3S,11E)-14,16-dihydroxy-3-methyl-3,4,5,6,9,10-hexahydro-1H-2-benzoxacyclotetradecine-1,7(8H)-dione · ligand · 2 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 | 219 | 0.86 | 0.97 | 22 | ZER |
| 2 | 211 | 0.85 | 0.97 | 25 | ZER |
| 3 | 77 | 0.63 | 0.90 | 17 | empty |
| 4 | 73 | 0.61 | 0.90 | 18 | empty |
| 5 | 204 | 0.50 | 0.76 | 22 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1635 Ų buried · 22 hydrogen bonds · protein-protein
- A–D · 525 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 511 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 5KRC · Crystal Structure of the ER-alpha Ligand-binding Domain (Y537S) in Complex with Zearale · 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
- Elsewhere: RCSB PDB 5KRC · PDBe 5KRC · UniProt P03372
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