SMTL ID : 9nnf.1

Cryo-EM structure of a de-novo designed binder NY1-B04 in complex with HLA-A*02:01 and NY-ESO-1-derived peptide SLLMWITQC

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 3.80 Å

Oligo State

hetero-1-1-1-mer

Ligands

1 x SER- LEU- LEU- MET- TRP- ILE- THR- GLN- CYS: NY-ESO-1-derived peptide SLLMWITQC(Non-covalent)

SER-LEU-LEU-MET-TRP-ILE-THR-GLN-CYS.1: 39 residues within 4Å: Chain A: E.96, A.97, S.103, M.104, Y.107, E.115, Q.118, Q.119, V.122, F.123, G.126, L.127, A.130 Chain B: M.5, Y.7, F.9, E.63, K.66, V.67, H.70, T.73, V.76, D.77, T.80, Y.84, R.97, Y.99, Y.116, Y.123, T.143, K.146, W.147, V.152, Q.155, L.156, Y.159, T.163, W.167, Y.171 24 PLIP interactions: 19 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: B:Y.7, B:F.9, B:V.67, B:V.152, B:L.156, B:Y.159, A:Y.107 Hydrogen bonds: B:Y.7, B:K.66, B:K.66, B:D.77, B:D.77, B:T.80, B:Y.99, B:K.146, B:W.147, B:Q.155, B:Y.159, B:Y.171, A:E.96, A:E.115, A:Q.118, A:Q.119 Salt bridges: B:K.146

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Johansen, K.H. et al., De novo-designed pMHC binders facilitate T cell-mediated cytotoxicity toward cancer cells. Science (2025)

Release Date

2025-07-23

Peptides

De-novo designed binder NY1-B04: A
HLA class I histocompatibility antigen, A alpha chain: B
Beta-2-microglobulin: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

De-novo designed binder NY1-B04

HLA class I histocompatibility antigen, A alpha chain

Beta-2-microglobulin

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