MolNFT v1 · #143693 · protein
Crystal structure of a nanobody-stabilized active state of the kappa- opioid receptor
6B73 · Soluble cytochrome B562, kappa-type opioid receptor: “Crystal structure of a nanobody-stabilized active state of the kappa- opioid receptor”. X-ray diffraction, 3 ligands (CVV, CLR, OLA), 6 pockets (best druggability 0.78). MolNFT…
- PDB
- 6B73
- Type
- protein
- Length
- 798 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Soluble cytochrome B562, kappa-type opioid receptor; Nanobody
- UniProt
- P0ABE7, P41145
- Ligands
- CVV, CLR, OLA
- Pockets
- 6 · best druggability 0.78
Structure
x-ray diffraction · 4 distinct chains · 57% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Soluble cytochrome B562, kappa-type opioid receptor | protein | 281 | 80% helix, 3% strand | P0ABE7, P41145 |
| B | Soluble cytochrome B562, kappa-type opioid receptor | protein | 269 | 83% helix, 3% strand | P0ABE7, P41145 |
| C | Nanobody | protein | 126 | 2% helix, 44% strand | — |
| D | Nanobody | protein | 122 | 0% helix, 46% strand | — |
Ligands and binding sites
- CVV · N-[(5alpha,6beta)-17-(cyclopropylmethyl)-3-hydroxy-7,8-didehydro-4,5-epoxymorphinan-6-yl]-3-iodobenzamide · ligand · 2 copies · chains A, B
- CLR · Cholesterol · ligand · 2 copies · chains A, B
- OLA · Oleic acid · ligand · 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, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1108 | 0.78 | 0.80 | 89 | CVV |
| 2 | 568 | 0.77 | 0.83 | 55 | CVV |
| 3 | 562 | 0.73 | 0.81 | 60 | empty |
| 4 | 207 | 0.60 | 0.81 | 28 | empty |
| 5 | 123 | 0.52 | 0.81 | 24 | empty |
Interfaces
5 interfaces between chains.
- B–C · 1115 Ų buried · 5 hydrogen bonds · protein-protein
- A–D · 1057 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 465 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 70 Ų buried · 3 hydrogen bonds · protein-protein
- B–D · 51 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 6B73 · Crystal Structure of a nanobody-stabilized active state of the kappa-opioid receptor · the same entry in another collection · chain D against D, TM-score 1.00
- P41145 · AlphaFold monomer V2.0 prediction for kappa-type opioid receptor (P41145) · a predicted model of the same protein · chain A against A, TM-score 0.90
- P0ABE7 · AlphaFold monomer V2.0 prediction for soluble cytochrome B562 (P0ABE7) · a predicted model of the same protein · chain B against A, TM-score 0.29
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
- Every structure of UniProt P41145
- Elsewhere: RCSB PDB 6B73 · PDBe 6B73 · UniProt P0ABE7 · UniProt P41145
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