CPL — combinatorial peptide library structures (cpl_structures.tar.gz)
7 TCR clones (1e6, 4c6, 868, ila1, mel5, mel8, sb27), best- vs worst-peptide AlphaFold C-beta peptide-swap models — 2103 PDB files (per-clone best/worst dirs inside the archive).
All seven clones now carry a model of their OWN cognate epitope in the best half: 1e6/ALWGPDPAAA, 4c6/LWMRLLPLL, 868/SLYNTVATL, ila1/ILAKFLHWL, mel5/ELAGIGILTV, mel8/EAAGIGILTV, sb27/LPEPLPQGQLTAY. The sb27 one (added 2026-07-27) was modelled after the other 2102 on the same receptor and MHC coordinates — chains A/B/D are byte-for-byte the other sb27 models', only the 13-mer peptide differs — but it is NOT part of the original library deposit, so anything that counts "structures per clone" should mark it separately.
868's cognate is SLYNTVATL (HIV-1 Gag p17 SL9), NOT SIFLFIARV. SIFLFIARV is one of its own library peptides and was recorded as the cognate until 2026-07-27; because the clone → crystal lookup was keyed on that string it matched nothing, and the pipeline reported that 868 had no deposited crystal. It has four: 5NME (the index complex, SLYNTVATL), 5NMD (unligated receptor), 5NMF (6I) and 5NMG (3F6I8V).
cpl_native_structures.tar.gz — the deposited complexes
27 RCSB entries covering all seven clones. The cognate complex per clone is
1e6→3UTS, 4c6→7NMG, 868→5NME, ila1→5MEN, mel5→3HG1, mel8→7Q9B, sb27→2AK4; the rest are the same
receptors on variant peptides. MATCH ON THE RECEPTOR (CDR3α/CDR3β pair), never on the epitope: a
peptide identifies neither side uniquely, and EAAGIGILTV in particular occurs both in MEL8's own
7Q9B and in 4QOK, whose receptor is MEL5. 7Q9B is held here as PDB (transferred from Native2026);
it was previously mmCIF-only, which made it invisible to a *.pdb glob.
Peptide-ranking benchmark: AUC of -TCRen(TCR:peptide), best(+) vs worst(-), per clone and pooled. Provenance: structures COMPUTED (AF peptide-swap); best/worst labels from EXPERIMENTAL combinatorial peptide-library positional scans (Sewell/Cole lab; see DATASETS.md per-clone references). Source: aldan3 /projects/structures/CPL_data_to_hf/pdb_cpl/.