Research workbench
Orange species of bacteriorhodopsin from halobacterium salinarum
Analyse Orange species of bacteriorhodopsin from halobacterium salinarum in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4MD1
- Type
- protein
- Length
- 224 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bacteriorhodopsin
- UniProt
- P02945
- Ligands
- L2P, SQL, RET
- Pockets
- 1 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 75% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Bacteriorhodopsin | protein | 224 | 75% helix, 5% strand | P02945 |
Ligands and binding sites
- L2P · 2,3-di-phytanyl-glycerol · ligand · 18 copies · chains A
- SQL · (6E,10E,14E,18E)-2,6,10,15,19,23-hexamethyltetracosa-2, 6,10,14,18,22-hexaene · ligand · chains A
- RET · Retinal · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 113 | 0.78 | 0.97 | 24 | RET |
Modifications
Observed in the structure: 1 cofactor (retinal Schiff base).
Compared structures
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 P02945
- Elsewhere: RCSB PDB 4MD1 · PDBe 4MD1 · UniProt P02945
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