SMTL ID : 8vcy.1

Human TCR A2.13 in complex with DQ8-InsC8-15NPY

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

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

Ligands

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

NAG.1: 4 residues within 4Å: Chain A: V.119, N.121, E.169, W.171 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:V.119 Hydrogen bonds: A:E.169 NAG.3: 3 residues within 4Å: Chain B: N.19, E.22, R.23 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:R.23

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 5 residues within 4Å: Chain A: L.111, D.113, K.143, F.149 Chain B: R.149 No protein-ligand interaction detected (PLIP) GOL.4: 3 residues within 4Å: Chain B: H.81 Chain C: Q.2 Chain D: G.28 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:G.28, C:Q.2 GOL.5: 6 residues within 4Å: Chain D: D.123, S.124, K.125, S.126, S.127, D.128 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:S.124 Water bridges: D:S.124, D:K.129 GOL.9: 5 residues within 4Å: Chain E: S.20, F.67, N.69, R.71, E.73 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:S.20, E:N.69, E:E.73 GOL.10: 4 residues within 4Å: Chain E: E.160, V.161, H.162, S.163 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:H.162, E:H.162, E:S.163

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

PO4.6: 6 residues within 4Å: Chain B: K.65 Chain D: Y.45, I.47, H.48, T.55, N.56 6 PLIP interactions: 1 interactions with chain B, 5 interactions with chain D Salt bridges: B:K.65, D:H.48 Hydrogen bonds: D:Y.45, D:H.48, D:T.55, D:N.56 PO4.7: 5 residues within 4Å: Chain C: Q.2, V.3 Chain D: K.2, E.30, H.91 4 PLIP interactions: 2 interactions with chain D, 2 interactions with chain C Salt bridges: D:K.2, D:H.91 Hydrogen bonds: C:G.1, C:V.3 PO4.8: 6 residues within 4Å: Chain D: H.110, I.111, Q.112, D.165, F.166, K.167 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:Q.112, D:D.165, D:K.167 Water bridges: D:N.113, D:N.113 PO4.11: 4 residues within 4Å: Chain E: P.6, R.7, Y.8, Y.210 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:R.7, E:Y.8, E:Y.8

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tran, M.T. et al., A structural basis of T cell cross-reactivity to native and spliced self-antigens presented by HLA-DQ8. J.Biol.Chem. (2024)

Release Date

2024-08-07

Peptides

MHC class II HLA-DQ-alpha chain: A
MHC class II HLA-DQ-beta-1: B
Hybrid insulin peptide (HIP; InsC8-15-NPY68-74): C
T-CELL-RECEPTOR, TCR A2.13 alpha: D
T-CELL-RECEPTOR, TCR A2.13 beta: E

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

MHC class II HLA-DQ-alpha chain

MHC class II HLA-DQ-beta-1

Hybrid insulin peptide (HIP; InsC8-15-NPY68-74)

T-CELL-RECEPTOR, TCR A2.13 alpha

T-CELL-RECEPTOR, TCR A2.13 beta

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