MolNFT v1 · #155895 · protein
The crystal structure of cyanorhodopsin (cyr) N4075R from cyanobacteria tolypothrix sp. nies-4075
6LM1: “The crystal structure of cyanorhodopsin (cyr) N4075R from cyanobacteria tolypothrix sp. nies-4075”. X-ray diffraction, 7 ligands (R16, D12, D10), 12 pockets (best druggability 0.80). MolNFT v1 #155895 on GenesisL1: 3D structure…
- PDB
- 6LM1
- Type
- protein
- Length
- 678 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Rhodopsin
- UniProt
- A0A218QMM7
- Ligands
- R16, D12, D10, RET, C14, MG, NO3
- Pockets
- 12 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 79% helix, 2% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Rhodopsin | protein | 226 | 79% helix, 2% strand | A0A218QMM7 |
Ligands and binding sites
- R16 · Hexadecane · ligand · 9 copies · chains A, B, C
- D12 · Dodecane · ligand · 6 copies · chains A, B, C
- D10 · Decane · ligand · 4 copies · chains A, B
- RET · Retinal · ligand · 3 copies · chains A, B, C
- C14 · Tetradecane · ligand · 3 copies · chains A, B, C
- MG · Magnesium ion · metal · 3 copies · chains A, B, C
- NO3 · Nitrate ion · ion · 2 copies · chains C
- HEX · Hexane · additive · 20 copies · chains A, B, C
- OCT · N-octane · additive · 19 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 126 | 0.80 | 0.97 | 23 | RET |
| 2 | 126 | 0.79 | 0.97 | 24 | RET |
| 3 | 119 | 0.79 | 0.97 | 22 | RET |
| 4 | 776 | 0.71 | 0.76 | 74 | OCT, R16 |
| 5 | 604 | 0.68 | 0.77 | 60 | D12, R16, HEX, OCT |
Interfaces
3 interfaces between chains.
- A–C · 526 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 513 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 489 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 cofactor (retinal Schiff base).
Compared structures
- 6LM1 · The crystal structure of cyanorhodopsin (CyR) N4075R from cyanobacteria Tolypothrix 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 A0A218QMM7
- Elsewhere: RCSB PDB 6LM1 · PDBe 6LM1 · UniProt A0A218QMM7
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