Research workbench
Crystal structure of metarhodopsin II
Analyse Crystal structure of metarhodopsin II in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3PXO
- Type
- protein
- Length
- 326 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Rhodopsin
- UniProt
- P02699
- Ligands
- PLM, RET, NAG, BMA, MAN
- Pockets
- 6 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 71% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Rhodopsin | protein | 326 | 71% helix, 4% strand | P02699 |
Ligands and binding sites
- PLM · Palmitic acid · ligand · chains A
- RET · Retinal · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A
- BMA · beta-D-mannopyranose · sugar
- MAN · alpha-D-mannopyranose · sugar
- BOG · octyl beta-D-glucopyranoside · additive · 2 copies · 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 221 | 0.83 | 0.95 | 29 | RET |
| 2 | 115 | 0.54 | 0.82 | 20 | empty |
| 3 | 261 | 0.53 | 0.75 | 26 | empty |
| 4 | 101 | 0.51 | 0.82 | 26 | empty |
| 5 | 64 | 0.41 | 0.80 | 13 | empty |
Modifications
Observed in the structure: 2 glycan, 1 cofactor, 1 disulfide, 1 lipid (N-glycosylation, retinal Schiff base, disulfide, palmitoylation).
Compared structures
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 3PXO · PDBe 3PXO · UniProt P02699
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