MolNFT v1 · #76196 · protein
Crystal structure of natronomonas pharaonis sensory rhodopsin II in the active state
3QDC · Sensory rhodopsin-2: “Crystal structure of natronomonas pharaonis sensory rhodopsin II in the active state”. X-ray diffraction, 3 ligands (LFA, L2P, RET), 2 pockets (best druggability 0.76). MolNFT v1 #76196 on GenesisL1: 3D…
- 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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