MolNFT v1 · #123424 · protein
Structure of the SRII/HTRII complex in I212121 space group ("U" shape) - M state
5JJF · Sensory rhodopsin-2: “Structure of the SRII/HTRII complex in I212121 space group ("U" shape) - M state”. X-ray diffraction, 2 ligands (LFA, RET), 3 pockets (best druggability 0.78). MolNFT v1 #123424 on GenesisL1: 3D structure…
- PDB
- 5JJF
- Type
- protein
- Length
- 284 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sensory rhodopsin-2; Sensory rhodopsin II transducer
- UniProt
- P42196, P42259
- Ligands
- LFA, RET
- Pockets
- 3 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 80% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Sensory rhodopsin-2 | protein | 221 | 77% helix, 4% strand | P42196 |
| B | Sensory rhodopsin II transducer | protein | 63 | 89% helix, 0% strand | P42259 |
Ligands and binding sites
- LFA · Eicosane · ligand · 12 copies · chains A, B
- 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
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 143 | 0.78 | 0.94 | 28 | RET |
| 2 | 216 | 0.59 | 0.80 | 30 | LFA |
| 3 | 83 | 0.53 | 0.85 | 17 | BOG |
Interfaces
1 interface between chains.
- A–B · 966 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 cofactor (retinal Schiff base).
Compared structures
- 5JJF · Structure of the SRII/HtrII Complex in I212121 space group ("U" shape) - M 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
- P42259 · AlphaFold monomer V2.0 prediction for sensory rhodopsin II transducer (P42259) · a predicted model of the same protein · chain B against A, TM-score 0.95
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
- Every structure of UniProt P42259
- Elsewhere: RCSB PDB 5JJF · PDBe 5JJF · UniProt P42196 · UniProt P42259
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