Research workbench
Crystal structure of bovine rod opsin in complex with a nanobody
Analyse Crystal structure of bovine rod opsin in complex with a nanobody in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 8FD0
- Type
- protein
- Length
- 845 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.71
- Source
- Bos taurus; Lama glama
- Molecule
- Rhodopsin; Nanobody Nb2
- UniProt
- P02699
- Ligands
- NAG, MAN, BMA
- Pockets
- 13 · best druggability 0.81
Structure
x-ray diffraction · resolution 3.71 · 3 distinct chains · 59% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Rhodopsin | protein | 310 | 69% helix, 4% strand | P02699 |
| B | Rhodopsin | protein | 307 | 70% helix, 4% strand | P02699 |
| C, D | Nanobody Nb2 | protein | 114 | 3% helix, 40% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 9 copies · chains A, C, B, D
- MAN · alpha-D-mannopyranose · sugar · 4 copies · chains C, D
- BMA · beta-D-mannopyranose · sugar · 3 copies · chains C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 141 | 0.81 | 0.97 | 33 | empty |
| 2 | 141 | 0.80 | 0.96 | 28 | empty |
| 3 | 550 | 0.66 | 0.76 | 39 | empty |
| 4 | 152 | 0.61 | 0.84 | 24 | empty |
| 5 | 288 | 0.60 | 0.78 | 28 | empty |
Interfaces
3 interfaces between chains.
- B–D · 661 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 544 Ų buried · 1 hydrogen bond · protein-protein
- A–B · 515 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
- P02699 · AlphaFold monomer V2.0 prediction for rhodopsin (P02699) · a predicted model of the same protein · chain B against A, TM-score 0.92
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 P02699
- Elsewhere: RCSB PDB 8FD0 · PDBe 8FD0 · UniProt P02699
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