# Public reference figure: PDB 8T5E

## Published material

Vázquez Torres, S. et al. **De novo design of high-affinity binders of bioactive helical peptides.** Nature 626, 435–442 (2024). DOI: https://doi.org/10.1038/s41586-023-06953-1. Structure: https://www.rcsb.org/structure/8T5E. The paper identifies this crystal structure in Fig. 3d and Extended Data Table 2.

Coordinates: https://files.rcsb.org/download/8T5E.cif. Exact RCSB responses, URLs, UTC download times, byte counts and SHA-256 hashes are preserved in `download-receipt.json`. The coordinate SHA-256 is `19cc02095a47982e0b018b8bb3fd43ce3bd3cf8ce19217da4b84c974ef7ba409`. Cached inputs are reused, and a changed source fails verification rather than being silently adopted.

Selected model **1**, biological assembly **1**, chains **A and B**. Chain A (entity 1) is the designed **Bim_fulldiff** protein, a synthetic construct with 141 deposited residues (130 modeled). Chain B (entity 2) is a **BIM/Bcl-2-like protein 11 peptide segment**, 26 deposited residues (22 modeled), associated with UniProt O43521. Both label and author chain identifiers are A/B. Assembly 1 is author/PISA defined, with identity operation x,y,z on A+B, verified independently in the mmCIF and assembly API response; no crystal mates were generated. The experimental method is X-ray diffraction at **3.00 Å** resolution.

## Local work and interpretation

This new illustration and its contact highlighting were generated locally from the published coordinates. No new protein design, AlphaFold or Boltz prediction, laboratory experiment, or binding measurement was performed. The workflow panel describes a possible development process in which ExoMBridge supports modeling, inspection, comparison and records. It does not attribute the study's protein design or experimental results to ExoMBridge.

Contacts use **observed A–B non-hydrogen/non-deuterium atoms at distance ≤4.5 Å**, inclusive, in Cartesian coordinates. `atom_contacts.csv` contains **261 atom pairs**; `residue_contacts.csv` contains **49 unique residue pairs**, with minimum observed distances. These involve 26 designed-protein residues and 18 peptide residues. Atom rows preserve original zero-based CIF row indices and atom-site IDs; CSVs preserve label and author chain/residue identifiers, atom names, and elements. Distances are numerical calculations on rounded experimental coordinates, not measurements of binding strength, affinity, hydrogen bonds or function. Reference B factors are not pLDDT.

Only the two selected protein chains contribute. No H/D atoms, waters, nonpolymers, alternate conformers or additional models occur in this source. Occupancies are all 1. The deposited intra-chain A disulfide is retained (label Cys102–Cys106, author Cys99–Cys103); no A–B covalent connection is declared. No assertion about unannotated terminal tags is made.

Missing residues remain absent: A label 1–4,119–122,139–141; B label 1–3,26. A Glu label118/author115 also lacks CG,CD,OE1,OE2. The figure must not invent the internal missing A segment. Label and author numbering differ: A author=label−3; B author=label+138. Missing atoms/residues are not evidence of absent biological contacts.

## Verification and reproducibility

`analyze_reference.py` reuses ExoMBridge's `reference_inventory` and `_parse_structure` directly in read-only reference mode, with no service/database mutation. A local cell-list distance calculation is independently checked against an all-pairs scalar `math.dist` calculation from raw mmCIF columns for every cutoff from 3.0 to 5.0 Å at 0.25 Å intervals. `sensitivity.csv` reports both atom and unique-residue pair counts; the 4.5 Å figure cutoff is marked. A rigid rotation/translation preserves membership and distances; synthetic distances immediately below, exactly at and immediately above 4.5 Å verify inclusivity. `verification.json` records outcomes, versions and code/source hashes. These checks validate this coordinate calculation, not biological efficacy.

Scientific parser versions: Gemmi 0.6.5; ExoMBridge `molecular-analysis-v1`; local figure method `8t5e-reference-proximity-v1`; Python 3.12.3. Script SHA-256: `fe240a12478911c4eac97679db31f038dba7d8e76004ec25f11332d49b385bf9`. ExoMBridge parser SHA-256: `ca78d6aaf2717470ac65f8af058d3201e8fa08f58dc9c70d1cf62e9fe957bafd`.

From the site checkout, using the existing ExoMBridge Python environment:

```sh
/opt/exocortex/connector-venv/bin/python scripts/exombridge-reference/analyze_reference.py --exombridge-root /path/to/exocortex-alphafold3
```

The explicit root selects the installed project parser. No private paths, local configuration, credentials, model weights or private research outputs are included in these public source files.