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

3C11-DQ2-glia-a2 complex

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.40 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(Post Translational Modification)

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

1 x NAG- NAG- BMA- BMA- BMA- FUC- FUC: beta-D-mannopyranose-(1-3)-[beta-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)][alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose

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

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

NAG.3: 1 residues within 4Å: Chain A: N.80 No protein-ligand interaction detected (PLIP)

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

IPA.4: 4 residues within 4Å: Chain A: V.37, D.38, L.39, G.40 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.37, A:L.39 IPA.5: 1 residues within 4Å: Chain A: D.112 No protein-ligand interaction detected (PLIP) IPA.6: 4 residues within 4Å: Chain B: E.138, E.139, T.140, A.141 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.139, B:T.140, B:T.140, B:A.141 IPA.7: 8 residues within 4Å: Chain A: Q.59 Chain C: A.35, G.52, I.53, I.54, T.59, N.61 Chain D: Y.94 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:A.35, C:I.54 Hydrogen bonds: C:G.52, C:N.61 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 Hydrogen bonds: E:G.13 Hydrophobic interactions: B:Y.61, C:V.29 IPA.9: 8 residues within 4Å: Chain C: C.22, A.24, H.34, I.36, P.55, S.79, T.80, A.81 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:A.81 Hydrogen bonds: C:T.80 IPA.12: 3 residues within 4Å: Chain D: S.10, S.12, E.143 3 PLIP interactions: 3 interactions with chain D Water bridges: D:S.12, D:S.12, D:R.142

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

CL.10: 6 residues within 4Å: Chain C: V.2, G.27, T.28, R.30, S.31, R.100 Ligand excluded by PLIP CL.11: 1 residues within 4Å: Chain C: S.31 Ligand excluded by PLIP CL.13: 1 residues within 4Å: Chain D: D.50 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
A

B
B

C
H

D
G

E
C

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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