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The crystal structure of cyanorhodopsin (CyR) N2098R from cyanobacteria Calothrix sp. NIES-2098
Analyse The crystal structure of cyanorhodopsin (CyR) N2098R from cyanobacteria… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6LM0
- Type
- protein
- Length
- 709 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.65
- Source
- Calothrix sp. NIES-2098
- Molecule
- Rhodopsin
- UniProt
- A0A1Z4FUT4
- Ligands
- C14, RET, D10
- Pockets
- 14 · best druggability 0.81
Structure
x-ray diffraction · resolution 2.65 · 3 distinct chains · 78% helix, 2% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Rhodopsin | protein | 240 | 78% helix, 2% strand | A0A1Z4FUT4 |
| B | Rhodopsin | protein | 227 | 78% helix, 2% strand | A0A1Z4FUT4 |
| C | Rhodopsin | protein | 242 | 77% helix, 2% strand | A0A1Z4FUT4 |
Ligands and binding sites
- C14 · Tetradecane · ligand · 4 copies · chains A, B, C
- RET · Retinal · ligand · 3 copies · chains A, B, C
- D10 · Decane · ligand · 2 copies · chains A, B, C
- OCT · N-octane · additive · 4 copies · chains A, C, B
- HEX · Hexane · additive · 3 copies · chains A, C, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 128 | 0.81 | 0.98 | 22 | RET |
| 2 | 128 | 0.80 | 0.97 | 24 | RET |
| 3 | 127 | 0.79 | 0.97 | 25 | RET |
| 4 | 547 | 0.63 | 0.75 | 73 | HEX |
| 5 | 315 | 0.61 | 0.78 | 30 | OCT, C14 |
Interfaces
3 interfaces between chains.
- A–C · 921 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 823 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 679 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 cofactor (retinal Schiff base).
Compared structures
- 6LM0 · The crystal structure of cyanorhodopsin (cyr) N2098R from cyanobacteria calothrix sp.… · 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 A0A1Z4FUT4
- Elsewhere: RCSB PDB 6LM0 · PDBe 6LM0 · UniProt A0A1Z4FUT4
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