SMTL ID : 6xc9.2 (1 other biounit)

Immune receptor complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

hetero-1-1-1-1-mer

Ligands

1 x NAG- NAG- FUC: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-FUC.1: 3 residues within 4Å: Chain B: T.48, N.49, E.52 No protein-ligand interaction detected (PLIP)

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.179 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:D.113, A:K.143, A:K.143, B:R.179, B:R.179 GOL.3: 5 residues within 4Å: Chain A: Q.47, S.136, E.137, Y.153 Chain B: D.182 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.136, A:S.136, A:E.137 GOL.6: 5 residues within 4Å: Chain B: I.157, K.158, V.159, S.174, I.187 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:I.157, B:V.159, B:S.174, B:S.174 GOL.7: 9 residues within 4Å: Chain C: Q.125, S.135, C.137, W.179, S.180, S.183, D.184, F.185, C.187 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:Q.125, C:S.135, C:S.180, C:S.180, C:D.184, C:F.185 GOL.8: 5 residues within 4Å: Chain C: T.27, E.29, F.94, A.99, K.101 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:E.29, C:K.101 Water bridges: C:E.29

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

NAG.4: 5 residues within 4Å: Chain A: V.119, N.121, E.169, H.170, W.171 No protein-ligand interaction detected (PLIP) NAG.5: 1 residues within 4Å: Chain A: N.81 No protein-ligand interaction detected (PLIP)

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 chain fusion: B
T-CELL-RECEPTOR, A3.10-alpha chain: C
T-CELL-RECEPTOR, A3.10-beta chain: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
F

B
H

C
I

D
J

MHC class II HLA-DQ-alpha chain

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

T-CELL-RECEPTOR, A3.10-alpha chain

T-CELL-RECEPTOR, A3.10-beta chain

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