Research workbench
Structure of the human dopamine D3 receptor in complex with eticlopride
Analyse Structure of the human dopamine D3 receptor in complex with eticlopride in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3PBL
- Type
- protein
- Length
- 855 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- D(3) dopamine receptor, lysozyme chimera
- EC
- 3.2.1.17
- UniProt
- P35462, P00720
- Ligands
- ETQ, GLC
- Pockets
- 9 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 73% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | D(3) dopamine receptor, lysozyme chimera (EC 3.2.1.17) | protein | 432 | 73% helix, 2% strand | P35462, P00720 |
| B | D(3) dopamine receptor, lysozyme chimera (EC 3.2.1.17) | protein | 423 | 73% helix, 4% strand | P35462, P00720 |
Ligands and binding sites
- ETQ · 3-chloro-5-ethyl-N-{[(2S)-1-ethylpyrrolidin-2-yl]methyl}-6-hydroxy-2-methoxybenzamide · ligand · 2 copies · chains A, B
- GLC · alpha-D-glucopyranose · sugar · 4 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1183 | 0.83 | 0.83 | 99 | ETQ |
| 2 | 399 | 0.75 | 0.84 | 39 | ETQ |
| 3 | 386 | 0.64 | 0.78 | 37 | empty |
| 4 | 169 | 0.53 | 0.79 | 27 | empty |
| 5 | 245 | 0.49 | 0.74 | 27 | GLC |
Interfaces
1 interface between chains.
- A–B · 1444 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 3PBL · Structure of the human dopamine D3 receptor in complex with eticlopride · the same entry in another collection · chain A against A, TM-score 1.00
- P35462 · AlphaFold monomer V2.0 prediction for D(3) dopamine receptor (P35462) · a predicted model of the same protein · chain A against A, TM-score 0.68
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 P35462
- Every structure of UniProt P00720
- Elsewhere: RCSB PDB 3PBL · PDBe 3PBL · UniProt P35462 · UniProt P00720
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