ATP synthase peripheral stalk subunit d, mitochondrial (ATP5PD) is a 161-residue protein from Bos taurus. This is its AlphaFold structure prediction, created 1 Aug 2025. UniProt accession: P13620.
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The mean pLDDT of this model is 86.1 (confident 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 | 42% |
| 70 to 90 | Confident: backbone generally right | 52% |
| 50 to 70 | Low: treat with caution | 3% |
| Below 50 | Very low: often disordered regions | 3% |
What pLDDT means and how to read it
Subunit d, of the mitochondrial membrane ATP synthase complex (F(1)F(0) ATP synthase or Complex V) that produces ATP from ADP in the presence of a proton gradient across the membrane which is generated by electron transport complexes of the respiratory chain. ATP synthase complex consist of a soluble F(1) head domain - the catalytic core - and a membrane F(1) domain - the membrane proton channel. These two domains are linked by a central stalk rotating inside the F(1) region and a stationary peripheral stalk. During catalysis, ATP synthesis in the catalytic domain of F(1) is coupled via a rotary mechanism of the central stalk subunits to proton translocation (By similarity). In vivo, can…
Component of the ATP synthase complex composed at least of ATP5F1A/subunit alpha, ATP5F1B/subunit beta, ATP5MC1/subunit c (homooctamer), MT-ATP6/subunit a, MT-ATP8/subunit 8, ATP5ME/subunit e, ATP5MF/subunit f, ATP5MG/subunit g, ATP5MK/subunit k, ATP5MJ/subunit j, ATP5F1C/subunit gamma, ATP5F1D/subunit delta, ATP5F1E/subunit epsilon, ATP5PF/subunit F6, ATP5PB/subunit b, ATP5PD/subunit d,…
Mitochondrion, Mitochondrion inner membrane
Compare the prediction with experimentally determined structures of the same protein:
| PDB ID | Method | Resolution | Chains and residues |
|---|---|---|---|
| 2CLY | X-ray | 2.8 Å | B/E=2-161 |
| 2WSS | X-ray | 3.2 Å | U=2-119 |
| 6YY0 | EM | 3.23 Å | d=2-161 |
| 6ZQM | EM | 3.29 Å | d=2-161 |
| 9W2R | EM | 3.4 Å | d=2-161 |
| 6ZIT | EM | 3.49 Å | d=2-161 |
| 6ZBB | EM | 3.61 Å | d=2-161 |
| 6ZPO | EM | 4.0 Å | d=2-161 |
| 6ZQN | EM | 4.0 Å | d=2-161 |
| 9W2S | EM | 4.0 Å | d=2-161 |
| 9W2T | EM | 4.1 Å | d=110-160 |
| 6ZIQ | EM | 4.33 Å | d=2-161 |
| 6ZIU | EM | 6.02 Å | d=2-161 |
| 5FIK | EM | 6.4 Å | U=2-125 |
| 5ARA | EM | 6.7 Å | U=2-125 |
| 5FIL | EM | 7.1 Å | U=2-125 |
| 5ARH | EM | 7.2 Å | U=2-125 |
| 5ARE | EM | 7.4 Å | U=2-125 |
| 5ARI | EM | 7.4 Å | U=2-125 |
| 5FIJ | EM | 7.4 Å | U=2-125 |
Showing 20 of 30 experimental structures (best resolution first).
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