SMTL ID : 9min.1 (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: 35 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.78, N.82, Y.89 Ligands: GOL.5 33 PLIP interactions: 26 interactions with chain A, 7 interactions with chain C Hydrophobic interactions: A:Y.9, A:F.11, A:V.69, A:H.72, A:T.75, A:D.79, A:L.83, A:Y.101, A:T.145, A:W.149, A:L.158, A:Y.161, A:Y.161, C:V.52, C:Y.89 Hydrogen bonds: A:E.65, A:K.68, A:D.79, A:T.82, A:Y.86, A:Y.101, A:Y.101, A:Q.157, A:W.169, A:Y.173, A:Y.173, C:R.59, C:R.59, C:Y.89, C:Y.89 Water bridges: A:R.99, C:N.82 Salt bridges: A:K.148

10 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 7 residues within 4Å: Chain A: L.217, T.218, W.219, Q.226, T.227, T.230, L.232 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:W.219, A:W.219 GOL.3: 6 residues within 4Å: Chain A: R.8, F.10, Y.29, D.31, D.32 Ligands: GOL.4 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.8, A:D.32 Water bridges: A:D.31 GOL.4: 7 residues within 4Å: Chain A: A.213, T.235, P.237, F.243 Chain B: Y.28, S.59 Ligands: GOL.3 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Y.28, B:S.59 GOL.5: 8 residues within 4Å: Chain A: K.68, T.165, W.169 Chain C: E.45, Y.88, K.92 Ligands: SER-LEU-LEU-MET-TRP-ILE-THR-GLN-VAL.1, GOL.6 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.68, A:W.169 GOL.6: 8 residues within 4Å: Chain A: E.60, Y.61, G.64, E.65, K.68, W.169 Chain C: E.45 Ligands: GOL.5 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.65, A:E.65, A:K.68 GOL.7: 6 residues within 4Å: Chain B: T.75, D.78, E.79, Y.80, W.97, R.99 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:T.75, B:E.79, B:E.79, B:Y.80, B:R.99, B:R.99 GOL.8: 8 residues within 4Å: Chain B: D.36, I.37, E.38, N.85, H.86, V.87 Chain D: Q.44, D.46 6 PLIP interactions: 4 interactions with chain B, 2 interactions with chain D Hydrogen bonds: B:D.36, B:N.85, D:Q.44 Water bridges: B:E.38, B:V.87, D:D.46 GOL.9: 8 residues within 4Å: Chain A: R.23, I.25 Chain B: S.35, D.36, I.37, H.53, L.66, Y.68 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:R.23, B:Y.68, B:Y.68 Water bridges: B:H.53 GOL.10: 4 residues within 4Å: Chain B: K.43, I.48, E.71, Y.80 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:K.43, B:K.43, B:E.71 Water bridges: B:K.43 GOL.11: 3 residues within 4Å: Chain D: R.19, T.68, S.70 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:R.19, D:R.19, D:S.70 Water bridges: D:Q.81

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
A

B
B

C
D

D
E

HLA class I antigen

Beta-2-microglobulin

designed minibinder KH46

nanobody AD01

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