Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit… (PDE6D) is a 150-residue protein from Homo sapiens. This is its AlphaFold structure prediction, created 1 Aug 2025. UniProt accession: O43924.
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The mean pLDDT of this model is 96.3 (very high overall). pLDDT is AlphaFold's per-residue confidence score from 0 to 100. In MolViewer, choose the B-factor color scheme to color the model by pLDDT, because AlphaFold stores it in the B-factor column.
| pLDDT band | Meaning | Share of residues |
|---|---|---|
| Above 90 | Very high: backbone and side chains are usually accurate | 93% |
| 70 to 90 | Confident: backbone generally right | 6% |
| 50 to 70 | Low: treat with caution | 1% |
| Below 50 | Very low: often disordered regions | 0% |
What pLDDT means and how to read it
Promotes the release of prenylated target proteins from cellular membranes (PubMed:9712853). Modulates the activity of prenylated or palmitoylated Ras family members by regulating their subcellular location (PubMed:22002721, PubMed:23698361). Required for normal ciliary targeting of farnesylated target proteins, such as INPP5E (PubMed:24166846). Required for RAB28 localization to the cone cell outer segments in the retina (By similarity). Modulates the subcellular location of target proteins by acting as a GTP specific dissociation inhibitor (GDI) (By similarity). Increases the affinity of ARL3 for GTP by several orders of magnitude. Stabilizes ARL3-GTP by decreasing the nucleotide…
Interacts with the prenylated catalytic subunits of PDE6, an oligomer composed of two catalytic chains (PDE6A and PDE6B) and two inhibitory chains (gamma); has no effect on enzyme activity but promotes the release of the prenylated enzyme from cell membrane (By similarity). Interacts with prenylated GRK1 and GRK7 (By similarity). Interacts with prenylated Ras family members, including RAP2A and…
Cytoplasm, cytosol, Cytoplasmic vesicle membrane, Cytoplasm, cytoskeleton, cilium basal body
Compare the prediction with experimentally determined structures of the same protein:
| PDB ID | Method | Resolution | Chains and residues |
|---|---|---|---|
| 5ML3 | X-ray | 1.4 Å | B=2-150 |
| 4JV8 | X-ray | 1.45 Å | B=1-150 |
| 7Q9Q | X-ray | 1.45 Å | BBB=2-150 |
| 7PAD | X-ray | 1.49 Å | B=2-150 |
| 5ML2 | X-ray | 1.6 Å | B=2-150 |
| 9HMC | X-ray | 1.65 Å | A/B=1-150 |
| 3T5G | X-ray | 1.7 Å | B=1-150 |
| 4JVB | X-ray | 1.75 Å | B=1-150 |
| 1KSH | X-ray | 1.8 Å | B=1-150 |
| 9RP6 | X-ray | 1.8 Å | A=1-150 |
| 5F2U | X-ray | 1.85 Å | A/B=2-150 |
| 7PAE | X-ray | 1.85 Å | B=2-150 |
| 7Q9S | X-ray | 1.85 Å | AAA/BBB=1-150 |
| 4JV6 | X-ray | 1.87 Å | B=1-150 |
| 5ML6 | X-ray | 1.87 Å | B=2-150 |
| 4JHP | X-ray | 1.9 Å | B=1-150 |
| 5TAR | X-ray | 1.9 Å | B=3-150 |
| 9RP7 | X-ray | 1.9 Å | B=1-150 |
| 5X72 | X-ray | 1.95 Å | A=1-150 |
| 7QF9 | X-ray | 1.95 Å | AAA/BBB=2-150 |
Showing 20 of 40 experimental structures (best resolution first).
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