High mobility group protein B1 (HMGB1) is a 215-residue protein from Homo sapiens. This is its AlphaFold structure prediction, created 1 Aug 2025. UniProt accession: P09429.
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The mean pLDDT of this model is 76.8 (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 | 39% |
| 70 to 90 | Confident: backbone generally right | 32% |
| 50 to 70 | Low: treat with caution | 8% |
| Below 50 | Very low: often disordered regions | 21% |
What pLDDT means and how to read it
Multifunctional redox sensitive protein with various roles in different cellular compartments. In the nucleus is one of the major chromatin-associated non-histone proteins and acts as a DNA chaperone involved in replication, transcription, chromatin remodeling, V(D)J recombination, DNA repair and genome stability (PubMed:33147444). Proposed to be an universal biosensor for nucleic acids. Promotes host inflammatory response to sterile and infectious signals and is involved in the coordination and integration of innate and adaptive immune responses. In the cytoplasm functions as a sensor and/or chaperone for immunogenic nucleic acids implicating the activation of TLR9-mediated immune…
Interacts (fully reduced HMGB1) with CXCL12; probably in a 1:2 ratio involving two molecules of CXCL12, each interacting with one HMG box of HMGB1; inhibited by glycyrrhizin (PubMed:22370717). Associates with the TLR4:LY96 receptor complex (PubMed:20547845). Component of the RAG complex composed of core components RAG1 and RAG2, and associated component HMGB1 or HMGB2 (By similarity). Interacts…
Nucleus, Chromosome, Cytoplasm, Secreted, Cell membrane, Endosome, Endoplasmic reticulum-Golgi intermediate compartment, Endoplasmic reticulum
Compare the prediction with experimentally determined structures of the same protein:
| PDB ID | Method | Resolution | Chains and residues |
|---|---|---|---|
| 9CG9 | EM | 2.94 Å | K=1-215 |
| 6CIK | X-ray | 3.15 Å | N=1-163 |
| 6CG0 | EM | 3.17 Å | N=15-140 |
| 6CIM | X-ray | 3.6 Å | N=1-163 |
| 6OEM | EM | 3.6 Å | H/N=15-155 |
| 6OEO | EM | 3.69 Å | N=1-163 |
| 6CIJ | EM | 3.9 Å | N=1-163 |
| 6CIL | X-ray | 4.15 Å | N=1-163 |
| 6OEN | EM | 4.3 Å | H/N=1-163 |
| 8I9M | EM | 5.19 Å | A=89-163 |
| 2LY4 | NMR | A=2-84 | |
| 2RTU | NMR | A=1-84 | |
| 2YRQ | NMR | A=1-166 |
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