MolNFT v1 · #173309 · protein
Structure of marine actinobacteria clade rhodopsin (macr) in orange form in P1211 space group
7AVO · Bacteriorhodopsin: “Structure of marine actinobacteria clade rhodopsin (macr) in orange form in P1211 space group”. X-ray diffraction, 2 ligands (LFA, OLB), 6 pockets (best druggability 0.67). MolNFT v1 #173309 on GenesisL1: 3D…
- PDB
- 7AVO
- Type
- protein
- Length
- 434 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bacteriorhodopsin
- UniProt
- S5DM51
- Ligands
- LFA, OLB
- Pockets
- 6 · best druggability 0.67
Structure
x-ray diffraction · 1 distinct chain · 85% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Bacteriorhodopsin | protein | 217 | 85% helix, 0% strand | S5DM51 |
Ligands and binding sites
- LFA · Eicosane · ligand · 24 copies · chains A, B
- OLB · (2S)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate · ligand · chains A
- OLC · (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 734 | 0.67 | 0.75 | 45 | LFA |
| 2 | 67 | 0.41 | 0.80 | 13 | empty |
| 3 | 67 | 0.39 | 0.79 | 12 | empty |
| 4 | 58 | 0.36 | 0.78 | 11 | empty |
| 5 | 67 | 0.32 | 0.75 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 219 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (nonstandard).
Compared structures
- 7AVO · Structure of marine actinobacteria clade rhodopsin (MacR) in orange form in P1211 space… · 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 S5DM51
- Elsewhere: RCSB PDB 7AVO · PDBe 7AVO · UniProt S5DM51
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