SMTL ID : 7sg2.1 (1 other biounit)

XPA5 TCR in complex with HLA-DQ2-omega1

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.10 Å

Oligo State

hetero-1-1-1-1-1-mer

Ligands

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

NAG.1: 6 residues within 4Å: Chain A: Y.19, V.118, N.120, E.168, H.169, W.170 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:V.118 Hydrogen bonds: A:Y.19, A:N.120

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

EDO.2: 2 residues within 4Å: Chain A: C.47, E.136 No protein-ligand interaction detected (PLIP)

1 x ACT: ACETATE ION(Non-functional Binders)

ACT.3: 3 residues within 4Å: Chain A: E.87, N.113 Chain B: R.47 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:N.113 Salt bridges: B:R.47

2 x CA: CALCIUM ION(Non-covalent)

CA.4: 2 residues within 4Å: Chain B: T.198, E.200 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:T.198 CA.5: 4 residues within 4Å: Chain D: D.12, I.13, S.220, D.223 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:I.13, D:S.220

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ciacchi, L. et al., Structural basis of T cell receptor specificity and cross-reactivity of two HLA-DQ2.5-restricted gluten epitopes in celiac disease. J.Biol.Chem. (2022)

Release Date

2022-02-23

Peptides

HLA class II histocompatibility antigen, DQ alpha 1 chain: A
MHC class II HLA-DQ-beta-1: B
T-cell receptor, xpa5, alpha chain: C
T-cell receptor, xpa5, beta chain: D
DQ2-glia-omega1 peptide: E

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
D

D
E

E
C

HLA class II histocompatibility antigen, DQ alpha 1 chain

MHC class II HLA-DQ-beta-1

T-cell receptor, xpa5, alpha chain

T-cell receptor, xpa5, beta chain

DQ2-glia-omega1 peptide

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