Outer membrane protein assembly factor BamD (bamD) is a 245-residue protein from Escherichia coli (strain K12). This is its AlphaFold structure prediction, created 1 Aug 2025. UniProt accession: P0AC02.
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The mean pLDDT of this model is 91.0 (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 | 78% |
| 70 to 90 | Confident: backbone generally right | 11% |
| 50 to 70 | Low: treat with caution | 11% |
| Below 50 | Very low: often disordered regions | 0% |
What pLDDT means and how to read it
Part of the outer membrane protein assembly complex (Bam), which is involved in assembly and insertion of beta-barrel proteins into the outer membrane. Constitutes, with BamA, the core component of the assembly machinery. Probably involved in transient protein interactions. Efficient substrate folding and insertion into the outer membrane requires all 5 subunits (PubMed:20378773, PubMed:21823654, PubMed:27686148). A lateral gate may open between the first and last strands of the BamA beta-barrel that allows substrate to insert into the outer membrane; comparison of the structures of complete and nearly complete Bam complexes show there is considerable movement of all 5 proteins…
Part of the Bam complex, which is composed of the outer membrane protein BamA, and four lipoproteins BamB, BamC, BamD and BamE. Forms a subcomplex with BamC and BamE. Interacts directly with BamA. The Bam complex has the shape of a hat, with the BamA beta-barrel crown in the outer membrane and the periplasmic brim formed by the BamA POTRA domains and the 4 lipoproteins (PubMed:26744406,…
Cell outer membrane
Compare the prediction with experimentally determined structures of the same protein:
| PDB ID | Method | Resolution | Chains and residues |
|---|---|---|---|
| 2YHC | X-ray | 1.8 Å | A=29-245 |
| 3Q5M | X-ray | 2.6 Å | A=23-245 |
| 9CNW | EM | 2.6 Å | D=1-245 |
| 9HG6 | EM | 2.73 Å | D=20-245 |
| 9HG5 | EM | 2.82 Å | D=20-245 |
| 9HG7 | EM | 2.83 Å | D=20-245 |
| 9HG9 | EM | 2.88 Å | D=20-245 |
| 3TGO | X-ray | 2.9 Å | A/B=21-245 |
| 5D0O | X-ray | 2.9 Å | D=1-245 |
| 8PZV | EM | 2.9 Å | D=20-245 |
| 9HG8 | EM | 2.9 Å | D=20-245 |
| 8ADG | EM | 3.0 Å | D=1-245 |
| 9HE1 | EM | 3.0 Å | D=1-245 |
| 7NRI | EM | 3.03 Å | D=20-245 |
| 6LYS | X-ray | 3.05 Å | D=1-245 |
| 8BO2 | EM | 3.1 Å | D=1-245 |
| 9CNZ | EM | 3.1 Å | D=1-245 |
| 6LYQ | X-ray | 3.19 Å | D=1-245 |
| 6LYR | X-ray | 3.28 Å | D=1-245 |
| 8BVQ | EM | 3.3 Å | D=20-245 |
Showing 20 of 92 experimental structures (best resolution first).
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