SMTL ID : 9eji.1

Peptide-independent T cell receptor recognition of HLA-DQ2

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

hetero-1-1-1-1-1-mer

Ligands

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

NAG-NAG.1: 3 residues within 4Å: Chain A: N.120, E.168, W.170 No protein-ligand interaction detected (PLIP)

2 x GOL: GLYCEROL

GOL.2: 7 residues within 4Å: Chain A: F.56, D.57, F.60 Chain C: P.2, P.3, A.4, S.5 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:S.5, A:D.57 GOL.7: 6 residues within 4Å: Chain D: Q.96, K.97 Chain E: F.44, E.47, N.55, E.97 6 PLIP interactions: 2 interactions with chain D, 4 interactions with chain E Hydrogen bonds: D:Q.96, D:L.98, E:E.47, E:N.55 Water bridges: E:S.32, E:S.32

1 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose

NAG.3: 4 residues within 4Å: Chain B: T.18, N.19, E.22 Chain E: E.51 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain E Hydrophobic interactions: B:T.18 Hydrogen bonds: B:E.22, E:E.51

3 x ACT: ACETATE ION

ACT.4: 5 residues within 4Å: Chain B: R.70, V.78 Chain C: S.5, E.6, Q.7 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain C Water bridges: B:R.77 Salt bridges: B:R.70 Hydrophobic interactions: C:Q.7 Hydrogen bonds: C:E.6 ACT.5: 5 residues within 4Å: Chain D: E.7, Q.8, D.9, T.26, Y.72 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:E.7, D:Y.72 ACT.6: 4 residues within 4Å: Chain E: L.10, K.12, V.18, T.19 3 PLIP interactions: 3 interactions with chain E Hydrophobic interactions: E:L.10 Hydrogen bonds: E:T.19 Salt bridges: E:K.12

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lim, J.J. et al., WITHHELD AT REQUEST OF AUTHORS. To Be Published

Release Date

2025-03-26

Peptides

HLA class II histocompatibility antigen DQ alpha chain: A
HLA class II histocompatibility antigen DQ beta chain: B
glut-L1 peptide: C
G9 T cell receptor alpha chain: D
G9 T cell receptor beta chain: E

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

HLA class II histocompatibility antigen DQ alpha chain

HLA class II histocompatibility antigen DQ beta chain

glut-L1 peptide

G9 T cell receptor alpha chain

G9 T cell receptor beta chain

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