SMTL ID : 7n2q.2 (1 other biounit)

AS4.3-YEIH-HLA*B27

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

hetero-1-1-1-1-mer

Ligands

1 x LEU- ARG- VAL- MET- MET- LEU- ALA- PRO- PHE: YeiH protein(Non-covalent)

LEU-ARG-VAL-MET-MET-LEU-ALA-PRO-PHE.1: 35 residues within 4Å: Chain A: A.29, I.30, Y.31, F.95 Chain B: T.94, Y.95, S.96 Chain C: Y.7, H.9, T.24, E.45, Y.59, R.62, E.63, I.66, S.67, T.73, D.77, L.81, Y.84, L.95, Y.99, D.116, Y.123, T.143, K.146, W.147, V.152, Q.155, L.156, Y.159, E.163, W.167, Y.171 Ligands: SO4.9 38 PLIP interactions: 31 interactions with chain C, 3 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: C:Y.7, C:Y.59, C:I.66, C:D.77, C:L.81, C:L.95, C:Y.99, C:D.116, C:Y.123, C:T.143, C:W.147, C:Y.159, C:Y.159, C:W.167, A:Y.31, B:Y.95 Hydrogen bonds: C:Y.7, C:Y.7, C:T.24, C:T.24, C:T.24, C:R.62, C:R.62, C:E.63, C:E.63, C:S.67, C:D.77, C:Y.99, C:Q.155, C:Y.171, B:S.96, B:S.96, B:S.96 Water bridges: C:E.45, A:S.52, A:S.52 Salt bridges: C:E.45, C:K.146

3 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.2: 6 residues within 4Å: Chain A: I.7, P.8, V.20, N.22, R.72 Ligands: GOL.4 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:I.7 Hydrogen bonds: A:N.22, A:R.72, A:R.72 NAG.3: 4 residues within 4Å: Chain A: E.56, T.58, N.63, Y.76 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.56 NAG.6: 6 residues within 4Å: Chain B: R.15, S.62, A.63, Q.64, E.72, N.74 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:Q.64 Hydrogen bonds: B:R.15, B:S.62, B:E.72, B:N.74

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 5 residues within 4Å: Chain A: L.11, E.17, N.18, V.20 Ligands: NAG.2 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.17, A:N.18, A:V.20 GOL.7: 8 residues within 4Å: Chain A: F.98 Chain B: Y.30, S.91, A.93, Y.95, D.98, T.99, Q.100 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:S.91, B:A.93, B:Y.95, B:D.98, B:Q.100 Water bridges: B:A.93 GOL.8: 3 residues within 4Å: Chain B: P.5, K.6, H.7 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.6, B:H.7

3 x SO4: SULFATE ION(Non-functional Binders)

SO4.5: 4 residues within 4Å: Chain A: R.55, L.66, D.67, K.68 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.67, A:K.68 Water bridges: A:S.52, A:S.53 Salt bridges: A:R.55 SO4.9: 5 residues within 4Å: Chain A: F.98 Chain B: Q.45, R.52, A.53 Ligands: LEU-ARG-VAL-MET-MET-LEU-ALA-PRO-PHE.1 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.45 Salt bridges: B:R.52 SO4.10: 3 residues within 4Å: Chain C: Q.72, R.75, R.79 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:Q.72 Salt bridges: C:R.79

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yang, X. et al., Autoimmunity-associated T cell receptors recognize HLA-B*27-bound peptides. Nature (2022)

Release Date

2022-12-07

Peptides

AS4.3 T cell receptor alpha chain: A
AS4.3 T cell receptor beta chain: B
Human leukocyte antigen B27: C
Beta-2-microglobulin: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
E

B
G

C
H

D
I

AS4.3 T cell receptor alpha chain

AS4.3 T cell receptor beta chain

Human leukocyte antigen B27

Beta-2-microglobulin

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