Research workbench
Estrogen receptor alpha ligand binding domain in complex with estradiol and SRC2-BCP1
Analyse Estrogen receptor alpha ligand binding domain in complex with estradiol and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5WGQ
- Type
- protein
- Length
- 481 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Estrogen receptor; SRC2-BCP1
- UniProt
- P03372
- Ligands
- ACE, EST, NH2
- Pockets
- 9 · best druggability 0.84
Structure
x-ray diffraction · 4 distinct chains · 69% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Estrogen receptor | protein | 231 | 69% helix, 4% strand | P03372 |
| B | Estrogen receptor | protein | 229 | 68% helix, 4% strand | P03372 |
| E | SRC2-BCP1 | protein | 11 | 73% helix, 0% strand | — |
| F | SRC2-BCP1 | protein | 10 | 70% helix, 0% strand | — |
Ligands and binding sites
- ACE · Acetyl group · ligand · 2 copies · chains E, F
- EST · Estradiol · ligand · 2 copies · chains A, B
- NH2 · Amino group · ion · chains B, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 192 | 0.84 | 0.97 | 22 | EST |
| 2 | 176 | 0.84 | 0.98 | 21 | EST |
| 3 | 75 | 0.64 | 0.91 | 17 | empty |
| 4 | 54 | 0.64 | 0.94 | 19 | empty |
| 5 | 81 | 0.59 | 0.88 | 18 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1535 Ų buried · 27 hydrogen bonds · protein-protein
- B–E · 548 Ų buried · 7 hydrogen bonds · protein-protein
- A–F · 466 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified, 2 covalent, 2 isopeptide (nonstandard, covalent ligand, isopeptide).
Compared structures
- 5WGQ · Estrogen Receptor Alpha Ligand Binding Domain in Complex with Estradiol and SRC2-BCP1 · 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 0.99
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 5WGQ · PDBe 5WGQ · UniProt P03372
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