SMTL ID : 6xp6.2 (1 other biounit)

3C11-DQ2-glia-a2 complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

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

Ligands

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.1: 1 residues within 4Å: Chain A: N.80 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 5 residues within 4Å: Chain A: Y.19, N.120, E.168, W.170 Chain B: P.5 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:P.5

1 x NAG- NAG- BMA- BMA: beta-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-BMA.3: 2 residues within 4Å: Chain B: N.20, E.23 No protein-ligand interaction detected (PLIP)

5 x IPA: ISOPROPYL ALCOHOL(Non-functional Binders)

IPA.4: 4 residues within 4Å: Chain A: G.23, D.38, L.39, G.40 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.39 Hydrogen bonds: A:D.38, A:L.39, A:G.40 Water bridges: A:R.41 IPA.5: 3 residues within 4Å: Chain A: D.112, K.142, F.148 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.148 Hydrogen bonds: A:K.142 IPA.6: 6 residues within 4Å: Chain A: Q.59 Chain C: A.35, G.52, I.53, N.61 Chain D: Y.94 5 PLIP interactions: 2 interactions with chain D, 3 interactions with chain C Hydrophobic interactions: D:Y.94, C:A.35 Water bridges: D:Y.94, C:I.36 Hydrogen bonds: C:N.61 IPA.7: 8 residues within 4Å: Chain C: C.22, A.24, H.34, I.36, P.55, S.79, T.80, A.81 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:A.24, C:I.36, C:P.55 Water bridges: C:S.31, C:H.34 IPA.8: 5 residues within 4Å: Chain B: Y.61 Chain C: T.28, V.29 Chain E: P.12, G.13 3 PLIP interactions: 1 interactions with chain E, 1 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: E:P.12, B:Y.61 Hydrogen bonds: C:V.29

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.9: 4 residues within 4Å: Chain C: V.2, G.27, T.28, R.100 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Frick, R. et al., A high-affinity human TCR-like antibody detects celiac disease gluten peptide-MHC complexes and inhibits T cell activation. Sci Immunol (2021)

Release Date

2021-07-28

Peptides

MHC class II HLA-DQ-alpha chain: A
MHC class II HLA-DQ-beta-1: B
3.C11 IgH Fab: C
3.C11 IgK Fab: D
DQ2-glia-a2 peptide: E

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

B
E

C
J

D
I

E
F

MHC class II HLA-DQ-alpha chain

MHC class II HLA-DQ-beta-1

3.C11 IgH Fab

3.C11 IgK Fab

DQ2-glia-a2 peptide

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