MolNFT v1 · #167351 · protein
Nanobody-enabled monitoring of kappa opioid receptor states
6VI4: “Nanobody-enabled monitoring of kappa opioid receptor states”. X-ray diffraction, 2 ligands (JDC, CLR), 8 pockets (best druggability 0.78). MolNFT v1 #167351 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6VI4
- Type
- protein
- Length
- 794 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Kappa opioid receptor; Nanobody 6
- UniProt
- P41145
- Ligands
- JDC, CLR
- Pockets
- 8 · best druggability 0.78
Structure
x-ray diffraction · 4 distinct chains · 57% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Kappa opioid receptor | protein | 283 | 78% helix, 4% strand | P41145 |
| B | Kappa opioid receptor | protein | 276 | 82% helix, 4% strand | P41145 |
| C | Nanobody 6 | protein | 118 | 3% helix, 58% strand | — |
| D | Nanobody 6 | protein | 117 | 3% helix, 59% strand | — |
Ligands and binding sites
- JDC · (3R)-7-hydroxy-N-{(2S)-1-[(3R,4R)-4-(3-hydroxyphenyl)-3,4-dimethylpiperidin-1-yl]-3-methylbutan-2-yl}-1,2,3, 4-tetrahydroisoquinoline-3-carboxamide · ligand · 2 copies · chains A, B
- CLR · Cholesterol · ligand · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 634 | 0.78 | 0.83 | 42 | JDC |
| 2 | 634 | 0.77 | 0.83 | 47 | JDC |
| 3 | 456 | 0.64 | 0.77 | 43 | empty |
| 4 | 288 | 0.57 | 0.76 | 23 | empty |
| 5 | 116 | 0.44 | 0.77 | 13 | empty |
Interfaces
3 interfaces between chains.
- A–D · 641 Ų buried · 13 hydrogen bonds · protein-protein
- B–C · 613 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 342 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
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 P41145
- Elsewhere: RCSB PDB 6VI4 · PDBe 6VI4 · UniProt P41145
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