Outer membrane protein A (ompA) is a 346-residue protein from Escherichia coli (strain K12). This is its AlphaFold structure prediction, created 1 Aug 2025. UniProt accession: P0A910.
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The mean pLDDT of this model is 79.5 (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 | 34% |
| 70 to 90 | Confident: backbone generally right | 44% |
| 50 to 70 | Low: treat with caution | 13% |
| Below 50 | Very low: often disordered regions | 9% |
What pLDDT means and how to read it
With TolR probably plays a role in maintaining the position of the peptidoglycan cell wall in the periplasm (Probable). Plays a role in resistance to environmental stress, and a role in outer membrane functionality and cell shape (PubMed:11906175, PubMed:361695). Non-covalently binds peptidoglycan (Probable) (PubMed:25135663). Acts as a porin with low permeability that allows slow penetration of small solutes (PubMed:1370823, PubMed:20004640, PubMed:21069910). A very abundant protein, there can be up to 210,000 OmpA molecules per cell (PubMed:24766808). Reconstitution in unilamellar lipid vesicles shows only about 3% of the protein is in an open conformation, which allows diffusion of…
Monomer (PubMed:10764596, PubMed:1370823, PubMed:9808047). Homodimer (PubMed:16079137, PubMed:21697552, PubMed:24746938). Interacts with Lpp (PubMed:3013869). About 10% of the C-terminal periplasmic domain dimerizes when expressed without the N-terminal domain (PubMed:24746938, PubMed:25135663). Interacts with F plasmid-encoded TraN during conjugation (Probable) (PubMed:16272376)
Cell outer membrane
Compare the prediction with experimentally determined structures of the same protein:
| PDB ID | Method | Resolution | Chains and residues |
|---|---|---|---|
| 1QJP | X-ray | 1.65 Å | A=22-192 |
| 5M2Q | X-ray | 1.7 Å | A/B=1-22 |
| 9FZC | X-ray | 2.27 Å | A/B=22-191 |
| 1BXW | X-ray | 2.5 Å | A=22-192 |
| 6LYR | X-ray | 3.28 Å | P=180-188 |
| 6ITC | EM | 3.45 Å | B=2-26 |
| 3JBU | EM | 3.64 Å | z=1-24 |
| 1G90 | NMR | A=22-197 | |
| 2GE4 | NMR | A=22-197 | |
| 2JMM | NMR | A=23-197 | |
| 2MQE | NMR | A=201-346 |
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