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AlphaFold3 models of TNFR1-ICM11 complexes (A) Native TNFR1–TNF reference structure for epitope orientation (adapted from PDB: 1TNR ). The following contact residues defines TNF binding site: Lys18, Ser49, His52, Trp93, Glu95, Arg132, Lys143, Lys144, Glu42, Ser43, His55, Cys56, Cys59, Ser60, Lys61, Arg63, Lys64, Glu65, and Met66. (B–D) AF3 models for 1:1, 2×, and 3× TNFR1-ICM11 assemblies. The AF3 confidences are indicated in the figure: ipTM provides confidence in the interface quality, and pTM summarizes the overall complex topology. The resulting contact residues of the 1:1 complex are: Arg63, Glu65, His91, Tyr92, Trp93, Glu95, Asn96, Gln99, Phe101, Lys118, Arg132, Glu133, Glu135, Glu147, and Lys150. Shared TNFR1 hotspot residues shared by both TNF and ICM11: Arg63, Glu65, Trp93, Glu95, Arg132. Interface/contact residues were computed <t>via</t> <t>Molecular</t> Operating Environment <t>(MOE)</t> software.
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AlphaFold3 models of TNFR1-ICM11 complexes (A) Native TNFR1–TNF reference structure for epitope orientation (adapted from PDB: 1TNR ). The following contact residues defines TNF binding site: Lys18, Ser49, His52, Trp93, Glu95, Arg132, Lys143, Lys144, Glu42, Ser43, His55, Cys56, Cys59, Ser60, Lys61, Arg63, Lys64, Glu65, and Met66. (B–D) AF3 models for 1:1, 2×, and 3× TNFR1-ICM11 assemblies. The AF3 confidences are indicated in the figure: ipTM provides confidence in the interface quality, and pTM summarizes the overall complex topology. The resulting contact residues of the 1:1 complex are: Arg63, Glu65, His91, Tyr92, Trp93, Glu95, Asn96, Gln99, Phe101, Lys118, Arg132, Glu133, Glu135, Glu147, and Lys150. Shared TNFR1 hotspot residues shared by both TNF and ICM11: Arg63, Glu65, Trp93, Glu95, Arg132. Interface/contact residues were computed <t>via</t> <t>Molecular</t> Operating Environment <t>(MOE)</t> software.
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AlphaFold3 models of TNFR1-ICM11 complexes (A) Native TNFR1–TNF reference structure for epitope orientation (adapted from PDB: 1TNR ). The following contact residues defines TNF binding site: Lys18, Ser49, His52, Trp93, Glu95, Arg132, Lys143, Lys144, Glu42, Ser43, His55, Cys56, Cys59, Ser60, Lys61, Arg63, Lys64, Glu65, and Met66. (B–D) AF3 models for 1:1, 2×, and 3× TNFR1-ICM11 assemblies. The AF3 confidences are indicated in the figure: ipTM provides confidence in the interface quality, and pTM summarizes the overall complex topology. The resulting contact residues of the 1:1 complex are: Arg63, Glu65, His91, Tyr92, Trp93, Glu95, Asn96, Gln99, Phe101, Lys118, Arg132, Glu133, Glu135, Glu147, and Lys150. Shared TNFR1 hotspot residues shared by both TNF and ICM11: Arg63, Glu65, Trp93, Glu95, Arg132. Interface/contact residues were computed <t>via</t> <t>Molecular</t> Operating Environment <t>(MOE)</t> software.
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AlphaFold3 models of TNFR1-ICM11 complexes (A) Native TNFR1–TNF reference structure for epitope orientation (adapted from PDB: 1TNR ). The following contact residues defines TNF binding site: Lys18, Ser49, His52, Trp93, Glu95, Arg132, Lys143, Lys144, Glu42, Ser43, His55, Cys56, Cys59, Ser60, Lys61, Arg63, Lys64, Glu65, and Met66. (B–D) AF3 models for 1:1, 2×, and 3× TNFR1-ICM11 assemblies. The AF3 confidences are indicated in the figure: ipTM provides confidence in the interface quality, and pTM summarizes the overall complex topology. The resulting contact residues of the 1:1 complex are: Arg63, Glu65, His91, Tyr92, Trp93, Glu95, Asn96, Gln99, Phe101, Lys118, Arg132, Glu133, Glu135, Glu147, and Lys150. Shared TNFR1 hotspot residues shared by both TNF and ICM11: Arg63, Glu65, Trp93, Glu95, Arg132. Interface/contact residues were computed via Molecular Operating Environment (MOE) software.

Journal: iScience

Article Title: Antigen-directed single domain antibody-based TNFR1 agonists elicit preferential killing of HER2-overexpressing cancer cells

doi: 10.1016/j.isci.2026.115327

Figure Lengend Snippet: AlphaFold3 models of TNFR1-ICM11 complexes (A) Native TNFR1–TNF reference structure for epitope orientation (adapted from PDB: 1TNR ). The following contact residues defines TNF binding site: Lys18, Ser49, His52, Trp93, Glu95, Arg132, Lys143, Lys144, Glu42, Ser43, His55, Cys56, Cys59, Ser60, Lys61, Arg63, Lys64, Glu65, and Met66. (B–D) AF3 models for 1:1, 2×, and 3× TNFR1-ICM11 assemblies. The AF3 confidences are indicated in the figure: ipTM provides confidence in the interface quality, and pTM summarizes the overall complex topology. The resulting contact residues of the 1:1 complex are: Arg63, Glu65, His91, Tyr92, Trp93, Glu95, Asn96, Gln99, Phe101, Lys118, Arg132, Glu133, Glu135, Glu147, and Lys150. Shared TNFR1 hotspot residues shared by both TNF and ICM11: Arg63, Glu65, Trp93, Glu95, Arg132. Interface/contact residues were computed via Molecular Operating Environment (MOE) software.

Article Snippet: molecular modeling software package MOE (Molecular Operating Environment) , Chemical Computing Group Inc. , RRID: SCR_014882.

Techniques: Binding Assay, Software