Research workbench
Xfel structure of the human delta opioid receptor in complex with a bifunctional peptide
Analyse Xfel 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
- 4RWD
- Type
- protein
- Length
- 809 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
- OLA, NA, NH2
- Pockets
- 10 · 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 | 401 | 82% helix, 3% strand | P0ABE7 |
| B | Soluble cytochrome B562,DELTA-type opioid receptor | protein | 400 | 82% helix, 3% strand | P0ABE7 |
| G, H | Bifunctional peptide | protein | 4 | 0% helix, 0% strand | — |
Ligands and binding sites
- OLA · Oleic acid · ligand · 7 copies · chains A, B
- NA · Sodium ion · metal · 2 copies · chains A, B
- NH2 · Amino group · ion · 2 copies · chains B, G, A, H
- OLC · (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 532 | 0.64 | 0.76 | 42 | empty |
| 2 | 436 | 0.63 | 0.76 | 38 | empty |
| 3 | 112 | 0.50 | 0.80 | 19 | empty |
| 4 | 166 | 0.46 | 0.76 | 29 | empty |
| 5 | 150 | 0.44 | 0.76 | 31 | empty |
Interfaces
3 interfaces between chains.
- B–G · 528 Ų buried · 3 hydrogen bonds · protein-protein
- A–B · 517 Ų buried · 8 hydrogen bonds · protein-protein
- A–H · 512 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified, 2 disulfide (nonstandard, disulfide).
Compared structures
- 4RWD · XFEL structure of the human delta opioid receptor in complex with a bifunctional peptide · 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 A against A, TM-score 0.26
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 4RWD · PDBe 4RWD · UniProt P0ABE7
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