Research workbench
Crystal structure of the proton pumping rhodopsin AR2 from marine alga acetabularia acetabulum
Analyse Crystal structure of the proton pumping rhodopsin AR2 from marine alga… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3AM6
- Type
- protein
- Length
- 896 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Rhodopsin-2
- Ligands
- CLR, RET
- Pockets
- 10 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 79% helix, 2% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Rhodopsin-2 | protein | 224 | 79% helix, 2% strand | — |
Ligands and binding sites
- CLR · Cholesterol · ligand · 8 copies · chains A, B, C, D
- RET · Retinal · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 965 | 0.82 | 0.83 | 69 | empty |
| 2 | 130 | 0.80 | 0.97 | 23 | RET |
| 3 | 127 | 0.80 | 0.97 | 23 | RET |
| 4 | 125 | 0.80 | 0.97 | 23 | RET |
| 5 | 129 | 0.79 | 0.96 | 24 | RET |
Interfaces
5 interfaces between chains.
- B–D · 591 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 585 Ų buried · 2 hydrogen bonds · protein-protein
- C–D · 295 Ų buried · 1 hydrogen bond · protein-protein
- A–B · 295 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 162 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 4 cofactor (retinal Schiff base).
Compared structures
- 3AM6 · Crystal structure of the proton pumping rhodopsin AR2 from marine alga Acetabularia… · 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
- Elsewhere: RCSB PDB 3AM6 · PDBe 3AM6
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