Research workbench
Crystal structure of natronomonas pharaonis sensory rhodopsin II in the active state
Analyse Crystal structure of natronomonas pharaonis sensory rhodopsin II in the active… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3QDC
- Type
- protein
- Length
- 219 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sensory rhodopsin-2
- UniProt
- P42196
- Ligands
- LFA, L2P, RET
- Pockets
- 2 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 79% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Sensory rhodopsin-2 | protein | 219 | 79% helix, 4% strand | P42196 |
Ligands and binding sites
- LFA · Eicosane · ligand · 29 copies · chains A
- L2P · 2,3-di-phytanyl-glycerol · ligand · 2 copies · chains A
- RET · Retinal · ligand · chains A
- BOG · octyl beta-D-glucopyranoside · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 133 | 0.76 | 0.94 | 25 | RET |
| 2 | 71 | 0.53 | 0.85 | 14 | LFA |
Modifications
Observed in the structure: 1 cofactor (retinal Schiff base).
Compared structures
- 3QDC · Crystal structure of Natronomonas pharaonis sensory rhodopsin II in the active state · the same entry in another collection · chain A against A, TM-score 1.00
- P42196 · AlphaFold monomer V2.0 prediction for sensory rhodopsin-2 (P42196) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 P42196
- Elsewhere: RCSB PDB 3QDC · PDBe 3QDC · UniProt P42196
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