MolNFT v1 · #123428 · protein
Structure of the SRII/HTRII complex in P64 space group ("U" shape)
5JJJ · Sensory rhodopsin-2: “Structure of the SRII/HTRII complex in P64 space group ("U" shape)”. X-ray diffraction, 2 ligands (LFA, RET), 3 pockets (best druggability 0.79). MolNFT v1 #123428 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5JJJ
- Type
- protein
- Length
- 276 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 0.79
Structure
x-ray diffraction · 2 distinct chains · 81% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Sensory rhodopsin-2 | protein | 216 | 78% helix, 4% strand | P42196 |
| B | Sensory rhodopsin II transducer | protein | 60 | 90% helix, 0% strand | P42259 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 138 | 0.79 | 0.95 | 27 | RET |
| 2 | 186 | 0.54 | 0.78 | 27 | LFA |
| 3 | 82 | 0.45 | 0.80 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 900 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 cofactor (retinal Schiff base).
Compared structures
- 5JJJ · Structure of the SRII/HtrII Complex in P64 space group ("U" shape) · 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 0.93
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 5JJJ · PDBe 5JJJ · UniProt P42196 · UniProt P42259
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