MolNFT v1 · #59826 · protein
Structure of a mutant bovine rhodopsin in hexagonal crystal form
3C9M: “Structure of a mutant bovine rhodopsin in hexagonal crystal form”. X-ray diffraction, 3 ligands (ACE, RET, NAG), 5 pockets (best druggability 0.82). MolNFT v1 #59826 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3C9M
- Type
- protein
- Length
- 326 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Rhodopsin
- UniProt
- P02699
- Ligands
- ACE, RET, NAG
- Pockets
- 5 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 64% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Rhodopsin | protein | 326 | 64% helix, 1% strand | P02699 |
Ligands and binding sites
- ACE · Acetyl group · ligand · chains A
- RET · Retinal · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 166 | 0.82 | 0.97 | 29 | RET |
| 2 | 91 | 0.41 | 0.78 | 18 | empty |
| 3 | 53 | 0.40 | 0.81 | 11 | empty |
| 4 | 54 | 0.29 | 0.74 | 11 | empty |
| 5 | 55 | 0.26 | 0.73 | 13 | empty |
Modifications
Observed in the structure: 2 disulfide, 1 cofactor, 1 covalent, 1 glycan (disulfide, retinal Schiff base, covalent ligand, N-glycosylation).
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 3C9M · PDBe 3C9M · UniProt P02699
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