MolNFT v2 · #209537 · protein
Crystal structure of photoactivated rhodopsin in complex with a nanobody
8FD1: “Crystal structure of photoactivated rhodopsin in complex with a nanobody”. X-ray diffraction at 4.25, 3 ligands (NAG, MAN, BMA). MolNFT v2 #209537 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- 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
- UniProt
- P02699
- Ligands
- NAG, MAN, BMA
Structure
x-ray diffraction · resolution 4.25 · 3 distinct chains.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | — | protein | 305 | — | P02699 |
| B | — | protein | 307 | — | P02699 |
| C, D | — | protein | 114 | — | — |
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.
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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