Research workbench
Crystal structure of the active delta opioid receptor in complex with the peptide agonist KGCHM07
Analyse Crystal structure of the active delta opioid receptor in complex with the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6PT2
- Type
- protein
- Length
- 766 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Delta opioid receptor; Peptide agonist KGCHM07
- Ligands
- OLA, OXJ, CLR
- Pockets
- 11 · best druggability 0.74
Structure
x-ray diffraction · 3 distinct chains · 79% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Delta opioid receptor | protein | 397 | 78% helix, 4% strand | — |
| B | Delta opioid receptor | protein | 361 | 82% helix, 4% strand | — |
| C, D | Peptide agonist KGCHM07 | protein | 4 | 0% helix, 0% strand | — |
Ligands and binding sites
- OLA · Oleic acid · ligand · 7 copies · chains A, B
- OXJ · 1-[3,5-bis(trifluoromethyl)phenyl]-N-methylmethanamine · ligand · 2 copies · chains A, C, B, D
- CLR · Cholesterol · ligand · chains A
- OLC · (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 689 | 0.74 | 0.80 | 64 | OXJ |
| 2 | 536 | 0.71 | 0.80 | 47 | OXJ |
| 3 | 293 | 0.65 | 0.81 | 40 | OLA |
| 4 | 130 | 0.64 | 0.87 | 22 | empty |
| 5 | 277 | 0.60 | 0.79 | 37 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1286 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 574 Ų buried · 0 hydrogen bonds · protein-protein
- B–D · 558 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 4 modified, 2 covalent, 2 d-amino, 2 disulfide (covalent ligand, D-amino acid, disulfide, methylation, nonstandard).
Compared structures
- 6PT2 · Crystal structure of the active delta opioid receptor in complex with the peptide agonist… · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Elsewhere: RCSB PDB 6PT2 · PDBe 6PT2
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