SMTL ID : 8vd0.2 (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

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

NAG.1: 6 residues within 4Å: Chain A: V.119, N.121, E.169, H.170, W.171 Ligands: NAG.2 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.121 NAG.2: 1 residues within 4Å: Ligands: NAG.1 No protein-ligand interaction detected (PLIP) NAG.6: 1 residues within 4Å: Chain B: N.40 No protein-ligand interaction detected (PLIP)

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 4 residues within 4Å: Chain A: S.142, K.143, S.144 Chain B: M.35 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.142 Water bridges: A:E.28, A:G.31, A:S.142, A:S.144 GOL.4: 4 residues within 4Å: Chain A: V.120, N.121, I.122, E.137 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.121, A:I.122, A:E.137 GOL.5: 5 residues within 4Å: Chain A: K.70, H.71, N.74 Chain B: G.16, G.17 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:G.16, A:K.70, A:N.74 GOL.7: 3 residues within 4Å: Chain B: D.97, H.102 Chain C: G.28 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain B Water bridges: C:G.28 Hydrogen bonds: B:H.102 GOL.8: 7 residues within 4Å: Chain C: M.1, K.2, T.3, T.4, N.22, H.23, S.24 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:N.22, C:S.24, C:S.24 Water bridges: C:T.25, C:T.25 GOL.9: 6 residues within 4Å: Chain C: N.113, I.114, Q.115, D.168, F.169, K.170 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:Q.115, C:K.170, C:K.170 Water bridges: C:N.116 GOL.11: 6 residues within 4Å: Chain D: P.6, L.9, K.11, Q.16, V.17, T.18 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:K.11, D:K.11, D:T.18, D:T.18 GOL.12: 6 residues within 4Å: Chain C: M.164, S.166 Chain D: S.164, G.165, R.191, V.192 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:R.191, C:S.166 Water bridges: D:S.193

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

PO4.10: 6 residues within 4Å: Chain B: K.86, E.90 Chain C: Y.45, I.47, H.48, N.56 5 PLIP interactions: 1 interactions with chain B, 4 interactions with chain C Salt bridges: B:K.86, C:H.48 Hydrogen bonds: C:H.48, C:H.48, C:N.56 PO4.13: 4 residues within 4Å: Chain D: E.161, V.162, H.163, S.164 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:H.163, D:S.164

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
F

B
H

C
I

D
J

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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