Research workbench
The crystal structure of the estrogen receptor DNA-binding domain bound to DNA: how receptors discriminate between their response elements
Analyse The crystal structure of the estrogen receptor DNA-binding domain bound to DNA… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1HCQ
- Type
- protein + DNA
- Length
- 362 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'- D(*CP*CP*AP*GP*GP*TP*CP*AP*CP*AP*GP*TP*GP*AP*CP*CP*T P*G)- 3'); DNA (5'…
- UniProt
- P03372
- Ligands
- ZN
- Pockets
- 3 · best druggability 0.69
Structure
x-ray diffraction · 5 distinct chains · 31% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C, G | DNA (5'- D(*CP*CP*AP*GP*GP*TP*CP*AP*CP*AP*GP*TP*GP*AP*CP*CP*T P*G)- 3') | dna | 18 | — | — |
| D, H | DNA (5'- D(*CP*CP*AP*GP*GP*TP*CP*AP*CP*TP*GP*TP*GP*AP*CP*CP*T P*G)- 3') | dna | 18 | — | — |
| A, E | Protein (estrogen receptor) | protein | 74 | 30% helix, 11% strand | P03372 |
| B | Protein (estrogen receptor) | protein | 71 | 34% helix, 11% strand | P03372 |
| F | Protein (estrogen receptor) | protein | 71 | 31% helix, 14% strand | P03372 |
Ligands and binding sites
- ZN · Zinc ion · metal · 8 copies · chains A, B, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 714 | 0.69 | 0.77 | 47 | empty |
| 2 | 485 | 0.66 | 0.78 | 37 | empty |
| 3 | 55 | 0.25 | 0.73 | 13 | empty |
Interfaces
12 interfaces between chains.
- C–D · 801 Ų buried · 98 hydrogen bonds · nucleic-nucleic
- G–H · 798 Ų buried · 104 hydrogen bonds · nucleic-nucleic
- A–B · 456 Ų buried · 3 hydrogen bonds · protein-protein
- E–F · 413 Ų buried · 3 hydrogen bonds · protein-protein
- C–B · 397 Ų buried · 12 hydrogen bonds · protein-nucleic
Compared structures
- 1HCQ · The crystal structure of the estrogen receptor DNA-binding domain bound to DNA: how… · the same entry in another collection · chain F against F, 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 0.95
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 1HCQ · PDBe 1HCQ · UniProt P03372
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