SMTL ID : 8vcx.1

Human TCR A2.13 in complex with DQ8-InsCpep

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.59 Å

Oligo State

hetero-1-1-1-1-1-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: 4 residues within 4Å: Chain C: R.79, S.80, N.81 Chain D: L.53 No protein-ligand interaction detected (PLIP)

2 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.2: 3 residues within 4Å: Chain C: N.121, E.169, W.171 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 3 residues within 4Å: Chain D: N.19, E.22, R.23 No protein-ligand interaction detected (PLIP)

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

PO4.4: 7 residues within 4Å: Chain A: K.2, E.30, H.91 Chain C: R.56 Chain E: G.1, Q.2, V.3 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain E Salt bridges: A:K.2, A:H.91 Hydrogen bonds: E:V.3, E:V.3

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 5 residues within 4Å: Chain A: Y.45, H.48, E.54, T.55, N.56 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.45, A:H.48, A:T.55, A:N.56 GOL.6: 6 residues within 4Å: Chain A: G.42, P.43, Q.44 Chain B: F.100, G.101, P.102 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:G.42, B:G.101 GOL.7: 8 residues within 4Å: Chain A: S.40, Q.41 Chain B: R.7, Y.8, L.86, P.102, G.103, R.105 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:S.40, B:R.7, B:Y.8 GOL.8: 3 residues within 4Å: Chain B: G.1, I.24, Y.99 2 PLIP interactions: 2 interactions with chain B Water bridges: B:G.1, B:G.1 GOL.9: 4 residues within 4Å: Chain A: G.28 Chain D: D.76, H.81, Q.84 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:D.76

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

T-CELL-RECEPTOR, TCR A2.13 alpha: A
T-CELL-RECEPTOR, A2.13-beta chain: B
MHC class II HLA-DQ-alpha chain: C
MHC class II HLA-DQ-beta-1: D
Proinsulin C-peptide (InsC8-22): E

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

B
E

C
A

D
B

E
C

T-CELL-RECEPTOR, TCR A2.13 alpha

T-CELL-RECEPTOR, A2.13-beta chain

MHC class II HLA-DQ-alpha chain

MHC class II HLA-DQ-beta-1

Proinsulin C-peptide (InsC8-22)

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