SMTL ID : 8v51.1

Crystal structure of a HLA-B*35:01-NP10 with D1 TCR

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

hetero-1-1-1-1-mer

Ligands

1 x LEU- PRO- PHE- GLU- LYS- SER- THR- VAL- MET: LEU-PRO-PHE-GLU-LYS-SER-THR-VAL-MET(Non-covalent)

LEU-PRO-PHE-GLU-LYS-SER-THR-VAL-MET.1: 36 residues within 4Å: Chain A: M.5, Y.7, Y.9, R.62, N.63, I.66, F.67, T.69, N.70, T.73, E.76, S.77, N.80, L.81, Y.84, Y.99, Y.123, T.143, K.146, W.147, A.150, V.152, Q.155, L.156, Y.159, W.167, Y.171 Chain C: Y.29, G.92, G.93 Chain D: V.28, T.95, G.96, G.97, Q.98, E.99 41 PLIP interactions: 31 interactions with chain A, 5 interactions with chain C, 5 interactions with chain D Hydrophobic interactions: A:Y.7, A:I.66, A:F.67, A:T.73, A:E.76, A:L.81, A:Y.99, A:T.143, A:A.150, A:V.152, A:L.156, A:L.156, A:Y.159, A:W.167, C:Y.29, D:V.28 Hydrogen bonds: A:Y.7, A:T.69, A:T.73, A:S.77, A:N.80, A:Y.99, A:Y.99, A:Q.155, A:Y.159, A:Y.171, C:Y.29, C:G.93, D:T.95, D:G.97 Water bridges: A:Y.9, A:R.62, A:R.62, A:N.70, A:R.97, C:Y.29, C:Y.29, D:E.99, D:E.99 Salt bridges: A:R.62, A:K.146

1 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.2: 4 residues within 4Å: Chain A: E.19, P.20, T.71, R.75 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:P.20 Water bridges: A:E.19

1 x NA: SODIUM ION(Non-functional Binders)

NA.3: 3 residues within 4Å: Chain A: Q.87, H.93 Ligands: PO4.4 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.87, A:H.93

5 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.4: 3 residues within 4Å: Chain A: Q.87, S.88 Ligands: NA.3 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.88, A:S.88, A:G.91 PO4.5: 4 residues within 4Å: Chain C: Q.78, K.80, R.161 Ligands: PO4.6 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:Q.78 Salt bridges: C:K.80, C:R.161 PO4.6: 4 residues within 4Å: Chain C: R.58, Q.78, K.80 Ligands: PO4.5 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:Q.78 Water bridges: C:R.58 Salt bridges: C:R.58, C:K.80 PO4.7: 3 residues within 4Å: Chain D: S.60, R.62, E.83 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:S.60, D:S.60 Water bridges: D:D.61 Salt bridges: D:R.62 PO4.8: 4 residues within 4Å: Chain D: E.163, V.164, H.165, S.166 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:H.165, D:H.165, D:S.166

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Quinones-Parra, S. et al., Molecular determinants of cross-strain influenza A virus recognition by T-cell receptors. To Be Published

Release Date

2024-12-18

Peptides

HLA-B35: A
Beta-2-microglobulin: B
D1 TCR alpha chain: C
D1 TCR beta chain: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
D

D
E

HLA-B35

Beta-2-microglobulin

D1 TCR alpha chain

D1 TCR beta chain

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