SMTL ID : 6qzc.1

HLA-DR1 with the QAR Peptide

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.64 Å

Oligo State

hetero-1-1-1-mer

Ligands

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.1: 3 residues within 4Å: Chain A: T.118, R.162, E.164 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.162

4 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.2: 3 residues within 4Å: Chain A: A.62, K.65, A.66 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:A.66 EDO.3: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) EDO.5: 2 residues within 4Å: Chain B: Q.93, R.95 No protein-ligand interaction detected (PLIP) EDO.6: 7 residues within 4Å: Chain A: N.67 Chain B: L.12, E.29, C.31, W.62 Chain C: T.11, I.12 4 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A, 1 interactions with chain C Hydrogen bonds: B:E.29, B:E.29, A:N.67, C:I.12

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 5 residues within 4Å: Chain A: V.114, E.164, H.165, W.166 Chain B: M.1 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:V.114, B:M.1, B:M.1, B:M.1 Water bridges: A:H.165

1 x SO4: SULFATE ION(Non-functional Binders)

SO4.7: 4 residues within 4Å: Chain B: S.64, Q.65, K.66, D.67 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.66, B:D.67

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Greenshields-Watson, A. et al., CD4+T Cells Recognize Conserved Influenza A Epitopes through Shared Patterns of V-Gene Usage and Complementary Biochemical Features. Cell Rep (2020)

Release Date

2020-07-15

Peptides

HLA class II histocompatibility antigen, DR alpha chain: A
HLA class II histocompatibility antigen, DRB1-1 beta chain: B
M1-208-222-QAR-Peptide: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
AAA

B
BBB

C
CCC

HLA class II histocompatibility antigen, DR alpha chain

HLA class II histocompatibility antigen, DRB1-1 beta chain

M1-208-222-QAR-Peptide

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