MolNFT v1 · #117444 · protein
Structure of fully modified geranylgeranylated PDE6C peptide in complex with PDE6D
5E8F · Retinal rod rhodopsin-sensitive cgmp 3',5'-cyclic…: “Structure of fully modified geranylgeranylated PDE6C peptide in complex with PDE6D”. X-ray diffraction, 1 ligand (GER), 3 pockets (best druggability 0.86). MolNFT v1 #117444 on…
- PDB
- 5E8F
- Type
- protein
- Length
- 306 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Retinal rod rhodopsin-sensitive cgmp 3',5'-cyclic phosphodiesterase subunit delta; Cone…
- EC
- 3.1.4.35
- UniProt
- O43924, P51160
- Ligands
- GER
- Pockets
- 3 · best druggability 0.86
Structure
x-ray diffraction · 3 distinct chains · 15% helix, 59% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Retinal rod rhodopsin-sensitive cgmp 3',5'-cyclic phosphodiesterase subunit delta (EC 3.1.4.35) | protein | 147 | 15% helix, 60% strand | O43924 |
| C | Retinal rod rhodopsin-sensitive cgmp 3',5'-cyclic phosphodiesterase subunit delta (EC 3.1.4.35) | protein | 149 | 15% helix, 59% strand | O43924 |
| D, E | Cone cgmp-specific 3',5'-cyclic phosphodiesterase subunit alpha' (EC 3.1.4.35) | protein | 5 | 0% helix, 20% strand | P51160 |
Ligands and binding sites
- GER · Geran-8-yl geran · ligand · 2 copies · chains A, D, C, E
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 | 282 | 0.86 | 0.97 | 38 | GER |
| 2 | 286 | 0.86 | 0.96 | 34 | GER |
| 3 | 149 | 0.48 | 0.78 | 21 | empty |
Interfaces
3 interfaces between chains.
- C–E · 558 Ų buried · 8 hydrogen bonds · protein-protein
- A–D · 542 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 359 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 lipid, 2 modified (geranylgeranylation, nonstandard).
Compared structures
- 5E8F · Structure of Fully modified geranylgeranylated PDE6C Peptide in complex with PDE6D · the same entry in another collection · chain A against A, TM-score 1.00
- O43924 · AlphaFold monomer V2.0 prediction for retinal rod rhodopsin-sensitive cgmp 3',5'-cyclic… · a predicted model of the same protein · chain A against A, TM-score 0.97
- P51160 · AlphaFold monomer V2.0 prediction for cone cgmp-specific 3',5'-cyclic phosphodiesterase… · a predicted model of the same protein · chain D against A, TM-score 0.91
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 O43924
- Every structure of UniProt P51160
- Elsewhere: RCSB PDB 5E8F · PDBe 5E8F · UniProt O43924 · UniProt P51160
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