SMTL ID : 9min.2 (1 other biounit)

Structure of a designed minibinder to NYESO1-A*02:01

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.05 Å

Oligo State

hetero-1-1-1-1-mer

Ligands

1 x SER- LEU- LEU- MET- TRP- ILE- THR- GLN- VAL: Cancer/testis antigen 1(Non-covalent)

SER-LEU-LEU-MET-TRP-ILE-THR-GLN-VAL.1: 36 residues within 4Å: Chain A: M.7, Y.9, F.11, M.47, E.65, K.68, V.69, H.72, T.75, V.78, D.79, T.82, L.83, Y.86, R.99, Y.101, Y.118, T.145, K.148, W.149, V.154, Q.157, L.158, Y.161, W.169, Y.173 Chain C: L.48, L.49, V.52, N.56, R.59, E.75, E.78, N.82, Y.89 Ligands: GOL.2 32 PLIP interactions: 9 interactions with chain C, 23 interactions with chain A Hydrophobic interactions: C:V.52, C:E.78, C:Y.89, A:Y.9, A:F.11, A:V.69, A:T.75, A:D.79, A:L.83, A:Y.118, A:T.145, A:W.149, A:L.158, A:Y.161 Hydrogen bonds: C:R.59, C:R.59, C:E.78, C:N.82, C:Y.89, C:Y.89, A:E.65, A:K.68, A:D.79, A:Y.86, A:Y.101, A:Y.101, A:Q.157, A:W.169, A:Y.173, A:Y.173 Water bridges: A:D.79, A:D.79

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 10 residues within 4Å: Chain A: K.68, Y.161, T.165, W.169 Chain C: E.45, Y.88, Y.89, K.92 Ligands: SER-LEU-LEU-MET-TRP-ILE-THR-GLN-VAL.1, SER-LEU-LEU-MET-TRP-ILE-THR-GLN-VAL.1 6 PLIP interactions: 2 interactions with chain A, 4 interactions with chain C Hydrogen bonds: A:K.68, C:E.45, C:Y.89, C:K.92, C:K.92 Water bridges: A:E.65 GOL.3: 7 residues within 4Å: Chain A: D.32, A.213, T.235, P.237, F.243 Chain B: Y.28, Y.65 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:D.32, B:Y.28, B:Y.65 GOL.4: 9 residues within 4Å: Chain A: H.190, W.206, L.208, R.236, Q.244 Chain B: S.13, P.16, R.99, M.101 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:Q.244, B:S.13, B:R.99 Water bridges: B:A.17 GOL.5: 5 residues within 4Å: Chain B: K.43, I.48, E.71, F.72, Y.80 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:K.43, B:K.43, B:E.71 Water bridges: B:T.70 GOL.6: 3 residues within 4Å: Chain B: S.22, N.23, F.24 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.22 GOL.7: 3 residues within 4Å: Chain D: T.57, K.58, Y.59 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:T.57, D:Y.59, D:Y.59

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Householder, K.D. et al., De novo design and structure of a peptide-centric TCR mimic binding module. Science (2025)

Release Date

2025-08-06

Peptides

HLA class I antigen: A
Beta-2-microglobulin: B
designed minibinder KH46: C
nanobody AD01: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
F

B
G

C
I

D
J

HLA class I antigen

Beta-2-microglobulin

designed minibinder KH46

nanobody AD01

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