Prothrombin (F2) is a 618-residue protein from Mus musculus. This is its AlphaFold structure prediction, created 1 Aug 2025. UniProt accession: P19221.
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The mean pLDDT of this model is 83.6 (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 | 51% |
| 70 to 90 | Confident: backbone generally right | 29% |
| 50 to 70 | Low: treat with caution | 12% |
| Below 50 | Very low: often disordered regions | 8% |
What pLDDT means and how to read it
Thrombin, which cleaves bonds after Arg and Lys, converts fibrinogen to fibrin and activates factors V, VII, VIII, XIII, and, in complex with thrombomodulin, protein C. Functions in blood homeostasis, inflammation and wound healing (By similarity). Activates coagulation factor XI (F11); activation is promoted by the contact with negatively charged surfaces (By similarity). Triggers the production of pro-inflammatory cytokines, such as MCP-1/CCL2 and IL8/CXCL8, in endothelial cells (By similarity)
Heterodimer (named alpha-thrombin) of a light and a heavy chain; disulfide-linked. Forms a heterodimer with SERPINA5. In plasma, interacts (via N-terminus) with alpha-1-microglobulin; this interaction does not prevent the activation of prothrombin to thrombin
Compare the prediction with experimentally determined structures of the same protein:
| PDB ID | Method | Resolution | Chains and residues |
|---|---|---|---|
| 3HK3 | X-ray | 1.94 Å | A=317-360, B=361-618 |
| 2PUX | X-ray | 2.0 Å | A=317-360, B=361-618 |
| 2OCV | X-ray | 2.2 Å | A=319-346, B=361-618 |
| 3HKI | X-ray | 2.2 Å | A/D=317-360, B/E=361-618 |
| 3EDX | X-ray | 2.4 Å | A/C/E=317-360, B/D/F=361-618 |
| 3HK6 | X-ray | 3.2 Å | A/C=317-360, B/D=361-618 |
| 2PV9 | X-ray | 3.5 Å | A=317-360, B=361-618 |
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