Research workbench
Time-resolved serial femtosecond crystallography reveals early structural changes in channelrhodopsin: dark state structure
Analyse Time-resolved serial femtosecond crystallography reveals early structural… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7C86
- Type
- protein
- Length
- 296 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sensory opsin A,CHANNELRHODOPSIN (chr) chimera between CHR1 &
- UniProt
- Q8L435
- Ligands
- RET, NAG
- Pockets
- 5 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 62% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Sensory opsin A,CHANNELRHODOPSIN (chr) chimera between CHR1 & | protein | 296 | 62% helix, 10% strand | Q8L435 |
Ligands and binding sites
- RET · Retinal · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A
- OLC · (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate · additive · 9 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 172 | 0.80 | 0.95 | 25 | RET |
| 2 | 82 | 0.74 | 0.97 | 35 | empty |
| 3 | 202 | 0.56 | 0.79 | 21 | empty |
| 4 | 83 | 0.37 | 0.77 | 16 | empty |
| 5 | 67 | 0.29 | 0.73 | 15 | empty |
Modifications
Observed in the structure: 1 cofactor, 1 glycan (retinal Schiff base, N-glycosylation).
Compared structures
- 7C86 · Time-resolved serial femtosecond crystallography reveals early structural changes in… · the same entry in another collection · chain A against A, TM-score 1.00
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 Q8L435
- Elsewhere: RCSB PDB 7C86 · PDBe 7C86 · UniProt Q8L435
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