SMTL ID : 6xco.1

Immune receptor complex

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.90 Å

Oligo State

hetero-1-1-1-1-mer

Ligands

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

NAG.1: 2 residues within 4Å: Chain A: N.121, W.171 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:W.171 NAG.2: 1 residues within 4Å: Chain A: N.81 No protein-ligand interaction detected (PLIP) NAG.5: 1 residues within 4Å: Chain B: N.49 No protein-ligand interaction detected (PLIP)

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 1 residues within 4Å: Chain A: D.6 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Water bridges: B:N.49 Hydrogen bonds: A:D.6 GOL.6: 2 residues within 4Å: Chain B: E.65, P.82 No protein-ligand interaction detected (PLIP) GOL.7: 2 residues within 4Å: Chain C: R.13, Q.142 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:Q.142 GOL.8: 6 residues within 4Å: Chain A: D.58 Chain C: A.93, G.94, G.95, N.96, R.98 6 PLIP interactions: 5 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:A.93, C:G.95, C:N.96, C:N.96, C:R.98 Water bridges: A:D.58 GOL.9: 6 residues within 4Å: Chain D: Y.48, Q.53, K.56, F.63, S.64, G.65 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:Y.48, D:Y.48, D:Q.53, D:K.56, D:G.65 GOL.10: 4 residues within 4Å: Chain C: K.127 Chain D: V.123, E.125, A.235 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:V.123, D:E.125

1 x CAC: CACODYLATE ION(Non-covalent)

CAC.4: 6 residues within 4Å: Chain A: Q.47, S.136, E.137, T.138, Y.153 Chain B: G.181 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.47

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tran, M.T. et al., T cell receptor recognition of hybrid insulin peptides bound to HLA-DQ8. Nat Commun (2021)

Release Date

2021-07-14

Peptides

MHC class II HLA-DQ-alpha chain: A
Hybrid Insulin Peptide, MHC class II HLA-DQ-beta-1 fusion: B
T-CELL-RECEPTOR, A1.9-alpha chain: C
T-CELL-RECEPTOR, A1.9-beta chain: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
D

D
E

MHC class II HLA-DQ-alpha chain

Hybrid Insulin Peptide, MHC class II HLA-DQ-beta-1 fusion

T-CELL-RECEPTOR, A1.9-alpha chain

T-CELL-RECEPTOR, A1.9-beta chain

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