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Crystal structure of the cell-free synthesized membrane protein, acetabularia rhodopsin I, at 1.80 ångström
Analyse Crystal structure of the cell-free synthesized membrane protein, acetabularia… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5AX1
- Type
- protein
- Length
- 235 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Rhodopsin I
- UniProt
- G3CEP6
- Ligands
- OLB, D10, D12, RET, C14, R16
- Pockets
- 3 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 81% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Rhodopsin I | protein | 235 | 81% helix, 3% strand | G3CEP6 |
Ligands and binding sites
- OLB · (2S)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate · ligand · 2 copies · chains A
- D10 · Decane · ligand · 2 copies · chains A
- D12 · Dodecane · 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
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 | 127 | 0.79 | 0.97 | 23 | RET |
| 2 | 146 | 0.62 | 0.85 | 23 | empty |
| 3 | 52 | 0.38 | 0.80 | 13 | empty |
Modifications
Observed in the structure: 1 cofactor (retinal Schiff base).
Compared structures
- 5AX1 · 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 5AX1 · PDBe 5AX1 · UniProt G3CEP6
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