Research workbench
Structure of marine actinobacteria clade rhodopsin (macr) in orange form in P1211 space group
Analyse Structure of marine actinobacteria clade rhodopsin (macr) in orange form in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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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