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Crystal structure of photoactivated rhodopsin in complex with a nanobody
Analyse Crystal structure of photoactivated rhodopsin 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
- 8FD1
- Type
- protein
- Length
- 840 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 4.25
- Source
- Bos taurus; Lama glama
- Molecule
- Rhodopsin; Nanobody Nb2
- UniProt
- P02699
- Ligands
- NAG, MAN, BMA
- Pockets
- 12 · best druggability 0.81
Structure
x-ray diffraction · resolution 4.25 · 3 distinct chains · 59% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Rhodopsin | protein | 305 | 70% helix, 4% strand | P02699 |
| B | Rhodopsin | protein | 307 | 69% helix, 4% strand | P02699 |
| C, D | Nanobody Nb2 | protein | 114 | 0% 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
12 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 183 | 0.81 | 0.95 | 32 | empty |
| 2 | 173 | 0.80 | 0.95 | 33 | empty |
| 3 | 558 | 0.67 | 0.77 | 37 | empty |
| 4 | 297 | 0.60 | 0.78 | 27 | empty |
| 5 | 129 | 0.60 | 0.85 | 23 | empty |
Interfaces
3 interfaces between chains.
- B–D · 601 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 546 Ų buried · 0 hydrogen bonds · protein-protein
- A–B · 512 Ų buried · 3 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 8FD1 · PDBe 8FD1 · UniProt P02699
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