SMTL ID : 8cmi.3 (2 other biounits)

Human Leukocyte Antigen class II allotype DR1 presenting SARS-CoV-2 Omicron (BA.1) Spike peptide S761-775

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

hetero-1-1-1-mer

Ligands

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

EDO.1: 7 residues within 4Å: Chain A: I.9, D.26, G.29, P.140, R.141, E.142, R.147 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.26 EDO.2: 6 residues within 4Å: Chain A: V.117, N.119, E.167, H.168, W.169 Chain B: M.4 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:W.169, A:W.169, B:M.4 Water bridges: A:V.118, A:N.119 EDO.3: 4 residues within 4Å: Chain B: S.130, I.131, E.132, E.180 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.132, B:E.180, B:E.180 EDO.4: 4 residues within 4Å: Chain B: K.102, V.103, L.188, V.190 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:V.103

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

SO4.5: 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:V.28 Salt bridges: B:R.27, B:R.84 SO4.6: 1 residues within 4Å: Chain C: T.1 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:T.1, C:T.1, C:T.1

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
Spike protein S2': C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
G

B
H

C
I

HLA class II histocompatibility antigen, DR alpha chain

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

Spike protein S2'

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