Research workbench
Crystal structure of bos taurus opsin regenerated with 6-carbon ring retinal chromophore
Analyse Crystal structure of bos taurus opsin regenerated with 6-carbon ring retinal… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5TE5
- Type
- protein
- Length
- 348 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Rhodopsin
- UniProt
- P02699
- Ligands
- ACE, 7AB
- Pockets
- 3 · best druggability 0.85
Structure
x-ray diffraction · 1 distinct chain · 58% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Rhodopsin | protein | 348 | 58% helix, 3% strand | P02699 |
Ligands and binding sites
- ACE · Acetyl group · ligand · chains A
- 7AB · (2E)-{(4E)-4-[(3E)-4-(2,6,6-trimethylcyclohex-1-en-1-yl)but-3-en-2-ylidene]cyclohex-2-en-1-ylidene}acetaldehyde · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 244 | 0.85 | 0.96 | 29 | 7AB |
| 2 | 180 | 0.51 | 0.78 | 29 | empty |
| 3 | 74 | 0.45 | 0.82 | 13 | empty |
Modifications
Observed in the structure: 2 covalent, 1 disulfide (covalent ligand, disulfide).
Compared structures
- 5TE5 · Crystal structure of Bos taurus opsin regenerated with 6-carbon ring retinal chromophore · the same entry in another collection · chain A against A, TM-score 1.00
- P02699 · AlphaFold monomer V2.0 prediction for rhodopsin (P02699) · a predicted model of the same protein · chain A against A, TM-score 0.85
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 P02699
- Elsewhere: RCSB PDB 5TE5 · PDBe 5TE5 · UniProt P02699
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