MolNFT v1 · #153738 · protein
Crystal structure of the dts-motif rhodopsin from phaeocystis globosa virus 12T
6JO0 · Virrdts: “Crystal structure of the dts-motif rhodopsin from phaeocystis globosa virus 12T”. X-ray diffraction, 5 ligands (RET, D10, D12), 2 pockets (best druggability 0.81). MolNFT v1 #153738 on GenesisL1: 3D structure, binding…
- PDB
- 6JO0
- Type
- protein
- Length
- 224 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Virrdts
- UniProt
- G8DI69
- Ligands
- RET, D10, D12, OLB, PO4
- Pockets
- 2 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 83% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Virrdts | protein | 224 | 83% helix, 0% strand | G8DI69 |
Ligands and binding sites
- RET · Retinal · ligand · chains A
- D10 · Decane · ligand · chains A
- D12 · Dodecane · ligand · chains A
- OLB · (2S)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate · ligand · chains A
- PO4 · Phosphate ion · ion · chains A
- OCT · N-octane · additive · 6 copies · chains A
- HEX · Hexane · additive · 5 copies · chains A
- DD9 · nonane · additive · 3 copies · 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 | 153 | 0.81 | 0.97 | 26 | RET |
| 2 | 96 | 0.50 | 0.81 | 17 | OCT, OLB |
Modifications
Observed in the structure: 1 cofactor (retinal Schiff base).
Compared structures
- 6JO0 · Crystal structure of the DTS-motif rhodopsin from Phaeocystis globosa virus 12T · the same entry in another collection · chain A against A, TM-score 1.00
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 G8DI69
- Elsewhere: RCSB PDB 6JO0 · PDBe 6JO0 · UniProt G8DI69
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