SMTL ID : 8cmf.2 (1 other biounit)

Human Leukocyte Antigen class II allotype DR1 presenting SARS-CoV-2 nsp3 epitope (orf1ab)1350-1364

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

hetero-1-1-1-mer

Ligands

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

EDO.1: 4 residues within 4Å: Chain A: P.128, V.129, T.130, T.131 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.130, A:T.131 EDO.2: 5 residues within 4Å: Chain B: T.81, Y.82 Chain C: Y.5, I.6, L.7 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:T.81 EDO.3: 5 residues within 4Å: Chain B: E.26, R.27, V.28, V.79, R.84 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.26, B:V.28, B:R.84

1 x SIN: SUCCINIC ACID(Non-covalent)

SIN.4: 5 residues within 4Å: Chain B: S.46, D.47, V.48, G.49, R.76 2 PLIP interactions: 2 interactions with chain B Water bridges: B:S.46 Salt bridges: B:R.76

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chen, Y. et al., Structural definition of HLA class II-presented SARS-CoV-2 epitopes reveals a mechanism to escape pre-existing CD4 + T cell immunity. Cell Rep (2023)

Release Date

2023-07-26

Peptides

HLA class II histocompatibility antigen, DR alpha chain: A
Human leukocyte antigen DR beta chain allotype DR1 (DRB1*0101): B
SARS-Cov-2 nsp3 epitope (orf1ab)1350-1364: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

B
E

C
F

HLA class II histocompatibility antigen, DR alpha chain

Human leukocyte antigen DR beta chain allotype DR1 (DRB1*0101)

SARS-Cov-2 nsp3 epitope (orf1ab)1350-1364

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