SMTL ID : 8vd0.1 (1 other biounit)

Human TCR ET650-4 in complex with DQ8-InsC8-15-IAPP2

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

hetero-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: N.121, E.169, H.170, W.171 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.121, A:E.169 Water bridges: A:V.119, A:W.171 NAG.2: 1 residues within 4Å: Chain A: N.81 No protein-ligand interaction detected (PLIP)

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 4 residues within 4Å: Chain A: K.70, H.71, N.74 Chain B: G.16 3 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B, 1 interactions with chain D Hydrogen bonds: A:K.70, B:G.16 Water bridges: D:R.28 GOL.4: 3 residues within 4Å: Chain A: L.157, S.159 Ligands: PO4.5 2 PLIP interactions: 2 interactions with chain A Water bridges: A:L.157, A:S.159 GOL.7: 7 residues within 4Å: Chain C: N.116, D.118, D.139, F.169 Chain D: T.134, K.136, R.191 6 PLIP interactions: 3 interactions with chain C, 3 interactions with chain D Hydrogen bonds: C:N.116, C:D.118, C:D.139, D:T.134, D:K.136, D:R.191 GOL.9: 3 residues within 4Å: Chain D: D.112, N.114, K.115 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:N.114, D:K.115

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

PO4.5: 3 residues within 4Å: Chain A: S.126, Y.164 Ligands: GOL.4 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.126, A:S.126, A:S.126, A:Y.164 Water bridges: A:Y.164 PO4.6: 3 residues within 4Å: Chain B: H.102, Q.105 Chain C: G.28 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain B Water bridges: C:G.28, C:G.28 Salt bridges: B:H.102 PO4.8: 5 residues within 4Å: Chain B: K.86 Chain C: Y.45, I.47, H.48, N.56 7 PLIP interactions: 5 interactions with chain C, 2 interactions with chain B Hydrogen bonds: C:Y.45, C:Y.45, C:H.48, C:N.56 Salt bridges: C:H.48, B:K.86 Water bridges: B:K.86 PO4.10: 5 residues within 4Å: Chain C: R.165 Chain D: E.161, V.162, H.163, S.164 4 PLIP interactions: 3 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:E.161, D:H.163, D:S.164 Salt bridges: C:R.165

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
Hybrid insulin peptide (HIP; InsC8-15-IAPP74-80),MHC class II HLA-DQ-beta-1 chimera: B
T-CELL-RECEPTOR, TCR ET650-4 alpha: C
T-CELL-RECEPTOR, TCR ET650-4 beta: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

C
D

D
E

MHC class II HLA-DQ-alpha chain

Hybrid insulin peptide (HIP; InsC8-15-IAPP74-80),MHC class II HLA-DQ-beta-1 chimera

T-CELL-RECEPTOR, TCR ET650-4 alpha

T-CELL-RECEPTOR, TCR ET650-4 beta

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