MolNFT v1 · #113938 · protein
Crystal structure of the cell-free synthesized membrane protein, acetabularia rhodopsin I, at 1.52 ångström
5AX0: “Crystal structure of the cell-free synthesized membrane protein, acetabularia rhodopsin I, at 1.52 ångström”. X-ray diffraction, 6 ligands (OLB, D12, D10), 2 pockets (best druggability 0.80). MolNFT v1 #113938 on GenesisL1: 3D…
- PDB
- 5AX0
- Type
- protein
- Length
- 234 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Rhodopsin I
- UniProt
- G3CEP6
- Ligands
- OLB, D12, D10, RET, C14, R16
- Pockets
- 2 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 80% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Rhodopsin I | protein | 234 | 80% helix, 3% strand | G3CEP6 |
Ligands and binding sites
- OLB · (2S)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate · ligand · 3 copies · chains A
- D12 · Dodecane · ligand · 2 copies · chains A
- D10 · Decane · ligand · 2 copies · chains A
- RET · Retinal · ligand · chains A
- C14 · Tetradecane · ligand · chains A
- R16 · Hexadecane · ligand · 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 132 | 0.80 | 0.97 | 21 | RET |
| 2 | 71 | 0.39 | 0.78 | 14 | empty |
Modifications
Observed in the structure: 1 cofactor (retinal Schiff base).
Compared structures
- 5AX0 · Crystal Structure of the Cell-Free Synthesized Membrane Protein, Acetabularia Rhodopsin… · 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 G3CEP6
- Elsewhere: RCSB PDB 5AX0 · PDBe 5AX0 · UniProt G3CEP6
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