SMTL ID : 9ejg.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

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

NAG.1: 4 residues within 4Å: Chain A: V.118, N.120, E.168, W.170 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:V.118 Water bridges: A:Y.19 NAG.9: 2 residues within 4Å: Chain E: T.18, N.19 2 PLIP interactions: 2 interactions with chain E Hydrophobic interactions: E:T.18 Hydrogen bonds: E:N.19

5 x FMT: FORMIC ACID

FMT.2: 2 residues within 4Å: Chain A: I.3, S.143 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:I.3, A:S.143 FMT.3: 3 residues within 4Å: Chain A: D.112, K.142, F.148 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.142 FMT.4: 4 residues within 4Å: Chain C: E.5, V.6, V.99, F.100 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:V.6, C:F.100 Water bridges: C:E.5, C:T.102 FMT.7: 4 residues within 4Å: Chain D: S.85, A.86, L.109, T.110 1 PLIP interactions: 1 interactions with chain D Water bridges: D:D.151 FMT.10: 3 residues within 4Å: Chain E: Q.126, H.177, P.178 No protein-ligand interaction detected (PLIP)

2 x GOL: GLYCEROL

GOL.5: 7 residues within 4Å: Chain D: R.95, S.98, E.100 Chain E: V.44, G.45, E.46, R.72 9 PLIP interactions: 4 interactions with chain E, 5 interactions with chain D Hydrogen bonds: E:G.45, E:R.72, D:E.100, D:E.100 Water bridges: E:V.44, E:R.48, D:S.98, D:G.99, D:G.99 GOL.11: 8 residues within 4Å: Chain A: I.3, V.4, A.5 Chain E: Y.16, F.17, T.18, R.23, R.25 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:F.17, E:T.18, E:R.25

3 x ACT: ACETATE ION

ACT.6: 5 residues within 4Å: Chain C: L.98, F.100 Chain D: L.42, Q.43, F.44 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:L.98, C:F.100, D:F.44 ACT.8: 7 residues within 4Å: Chain D: T.4, Q.5, T.6, S.21, C.22, S.23, R.72 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:T.6, D:T.6, D:S.23 ACT.12: 4 residues within 4Å: Chain E: F.132, D.135, T.172, H.174 2 PLIP interactions: 2 interactions with chain E Hydrophobic interactions: E:T.172 Hydrogen bonds: E:D.135

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 1 chain: A
glia-omega 1 peptide: B
G9 T cell receptor alpha chain: C
G9 T cell receptor beta chain: D
MHC class II HLA-DQ-beta-1: E

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

C
D

D
E

E
B

HLA class II histocompatibility antigen, DQ alpha 1 chain

glia-omega 1 peptide

G9 T cell receptor alpha chain

G9 T cell receptor beta chain

MHC class II HLA-DQ-beta-1

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