Research workbench
Crystal structure of dtg rhodopsin from pseudomonas putida
Analyse Crystal structure of dtg rhodopsin from pseudomonas putida in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7W74
- Type
- protein
- Length
- 452 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bacteriorhodopsin-like protein
- UniProt
- A0A370SAH7
- Ligands
- RET, OLB
- Pockets
- 3 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 77% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Bacteriorhodopsin-like protein | protein | 226 | 77% helix, 3% strand | A0A370SAH7 |
Ligands and binding sites
- RET · Retinal · ligand · 2 copies · chains A, B
- OLB · (2S)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate · ligand · 2 copies · chains A, B
- OLC · (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate · additive · 5 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 136 | 0.80 | 0.96 | 23 | RET |
| 2 | 143 | 0.79 | 0.96 | 26 | RET |
| 3 | 227 | 0.56 | 0.78 | 28 | empty |
Interfaces
1 interface between chains.
- A–B · 284 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 cofactor (retinal Schiff base).
Compared structures
- 7W74 · Crystal structure of DTG rhodopsin from Pseudomonas putida · 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 A0A370SAH7
- Elsewhere: RCSB PDB 7W74 · PDBe 7W74 · UniProt A0A370SAH7
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