Research workbench
Synchrotron structure of the human delta opioid receptor in complex with a bifunctional peptide (psi community target)
Analyse Synchrotron structure of the human delta opioid receptor in complex with a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4RWA
- Type
- protein
- Length
- 788 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Soluble cytochrome B562,DELTA-type opioid receptor; Bifunctional peptide
- UniProt
- P0ABE7
- Ligands
- NH2
- Pockets
- 6 · best druggability 0.64
Structure
x-ray diffraction · 3 distinct chains · 81% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Soluble cytochrome B562,DELTA-type opioid receptor | protein | 391 | 81% helix, 3% strand | P0ABE7 |
| B | Soluble cytochrome B562,DELTA-type opioid receptor | protein | 389 | 81% helix, 3% strand | P0ABE7 |
| G, H | Bifunctional peptide | protein | 4 | 0% helix, 0% strand | — |
Ligands and binding sites
- NH2 · Amino group · ion · 2 copies · chains G, A, H
- OLC · (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 461 | 0.64 | 0.77 | 44 | NH2 |
| 2 | 387 | 0.61 | 0.77 | 46 | NH2 |
| 3 | 158 | 0.47 | 0.77 | 25 | empty |
| 4 | 86 | 0.34 | 0.74 | 18 | empty |
| 5 | 67 | 0.33 | 0.75 | 17 | empty |
Interfaces
3 interfaces between chains.
- A–B · 524 Ų buried · 8 hydrogen bonds · protein-protein
- A–H · 503 Ų buried · 4 hydrogen bonds · protein-protein
- B–G · 497 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified, 2 disulfide (nonstandard, disulfide).
Compared structures
- 4RWA · Synchrotron structure of the human delta opioid receptor in complex with a bifunctional… · the same entry in another collection · chain A against A, TM-score 1.00
- P0ABE7 · AlphaFold monomer V2.0 prediction for soluble cytochrome B562 (P0ABE7) · a predicted model of the same protein · chain B against A, TM-score 0.27
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 P0ABE7
- Elsewhere: RCSB PDB 4RWA · PDBe 4RWA · UniProt P0ABE7
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