SMTL ID : 6dig.1

Crystal structure of DQA1*01:02/DQB1*06:02 in complex with a hypocretin peptide

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

hetero-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 B: N.23, E.26, R.27 No protein-ligand interaction detected (PLIP)

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

NAG.2: 3 residues within 4Å: Chain A: R.79, N.81 Chain B: Q.57 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.57 NAG.3: 4 residues within 4Å: Chain A: N.121, E.169, H.170, W.171 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.121 Water bridges: A:H.170

1 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.4: 5 residues within 4Å: Chain A: L.111, D.113, K.143, F.149 Chain B: R.153 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:R.153, B:R.153, A:D.113 Water bridges: B:R.153

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jiang, W. et al., In vivo clonal expansion and phenotypes of hypocretin-specific CD4+T cells in narcolepsy patients and controls. Nat Commun (2019)

Release Date

2019-05-08

Peptides

MHC class II HLA-DQ-alpha chain: A
HLA class II histocompatibility antigen, DQ beta 1 chain: B
13-mer peptide: ALA-GLY-ASN-HIS-ALA-ALA-GLY-ILE-LEU-THR-LEU-GLY-LYS: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

MHC class II HLA-DQ-alpha chain

HLA class II histocompatibility antigen, DQ beta 1 chain

13-mer peptide: ALA-GLY-ASN-HIS-ALA-ALA-GLY-ILE-LEU-THR-LEU-GLY-LYS