MolNFT v1 · #123432 · protein
Structure of the SRII/HTRII(G83F) complex in P212121 space group ("V" shape)
5JJN · Sensory rhodopsin-2: “Structure of the SRII/HTRII(G83F) complex in P212121 space group ("V" shape)”. X-ray diffraction, 2 ligands (LFA, RET), 8 pockets (best druggability 0.76). MolNFT v1 #123432 on GenesisL1: 3D structure, binding…
- PDB
- 5JJN
- Type
- protein
- Length
- 560 residues
- Chains
- 4
- 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
- 8 · best druggability 0.76
Structure
x-ray diffraction · 3 distinct chains · 79% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Sensory rhodopsin-2 | protein | 223 | 78% helix, 4% strand | P42196 |
| B, D | Sensory rhodopsin II transducer | protein | 61 | 89% helix, 0% strand | P42259 |
| C | Sensory rhodopsin-2 | protein | 215 | 78% helix, 4% strand | P42196 |
Ligands and binding sites
- LFA · Eicosane · ligand · 15 copies · chains A, B, C, D
- RET · Retinal · ligand · 2 copies · chains A, C
- BOG · octyl beta-D-glucopyranoside · additive · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 125 | 0.76 | 0.94 | 24 | RET |
| 2 | 136 | 0.76 | 0.94 | 25 | RET |
| 3 | 110 | 0.59 | 0.85 | 19 | BOG |
| 4 | 212 | 0.53 | 0.77 | 27 | empty |
| 5 | 189 | 0.50 | 0.76 | 26 | empty |
Interfaces
3 interfaces between chains.
- B–D · 1176 Ų buried · 0 hydrogen bonds · protein-protein
- A–B · 879 Ų buried · 6 hydrogen bonds · protein-protein
- C–D · 858 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 cofactor (retinal Schiff base).
Compared structures
- 5JJN · Structure of the SRII/HtrII(G83F) Complex in P212121 space group ("V" 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 C 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 5JJN · PDBe 5JJN · UniProt P42196 · UniProt P42259
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