MolNFT v1 · #8398 · protein
Structure of bovine rhodopsin in a trigonal crystal form
1GZM: “Structure of bovine rhodopsin in a trigonal crystal form”. X-ray diffraction, 7 ligands (PLM, ACE, RET), 5 pockets (best druggability 0.82). MolNFT v1 #8398 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1GZM
- Type
- protein
- Length
- 656 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Rhodopsin
- UniProt
- P02699
- Ligands
- PLM, ACE, RET, PEF, NAG, BMA, ZN
- Pockets
- 5 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 69% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Rhodopsin | protein | 328 | 69% helix, 4% strand | P02699 |
Ligands and binding sites
- PLM · Palmitic acid · ligand · 4 copies · chains A, B
- ACE · Acetyl group · ligand · 2 copies · chains A, B
- RET · Retinal · ligand · 2 copies · chains A, B
- PEF · Di-palmitoyl-3-sn-phosphatidylethanolamine · ligand · 2 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains A, B
- BMA · beta-D-mannopyranose · sugar · 4 copies
- ZN · Zinc ion · metal · 2 copies · chains A, B
- C8E · (hydroxyethyloxy)tri(ethyloxy)octane · additive · 12 copies · chains A, B
- LDA · Lauryl dimethylamine-N-oxide · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 152 | 0.82 | 0.98 | 31 | RET |
| 2 | 138 | 0.80 | 0.97 | 29 | RET |
| 3 | 1150 | 0.76 | 0.78 | 104 | C8E, LDA |
| 4 | 133 | 0.41 | 0.75 | 22 | empty |
| 5 | 72 | 0.32 | 0.75 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 1085 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 glycan, 4 lipid, 2 cofactor, 2 covalent, 2 disulfide (N-glycosylation, palmitoylation, retinal Schiff base, covalent ligand, disulfide).
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 P02699
- Elsewhere: RCSB PDB 1GZM · PDBe 1GZM · UniProt P02699
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