SMTL ID : 8cmb.1

Human Leukocyte Antigen class II allotype DR1 presenting SARS-CoV-2 Spike peptide S486-505

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.84 Å

Oligo State

hetero-1-1-1-mer

Ligands

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

EDO.1: 6 residues within 4Å: Chain A: T.42, W.44, G.50, A.53, S.54, F.55 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.50, A:F.55, A:F.55 EDO.2: 7 residues within 4Å: Chain A: I.9, D.26, G.29, P.140, R.141, E.142, R.147 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.26, A:R.141 Water bridges: A:E.142 EDO.3: 8 residues within 4Å: Chain A: R.124, F.154, L.155, P.156, S.157, D.160, Y.162, W.179 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.157, A:S.157 Water bridges: A:R.124, A:L.155 EDO.4: 3 residues within 4Å: Chain B: V.146, V.147, S.148 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:V.146, B:S.148 EDO.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, B:R.84, B:R.84 EDO.6: 6 residues within 4Å: Chain B: E.180, H.181, V.184, T.185, S.186, P.187 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:H.181, B:H.181 EDO.7: 4 residues within 4Å: Chain B: R.43, D.45, V.48, R.52 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.29, B:R.43, B:D.45, B:D.45 EDO.8: 4 residues within 4Å: Chain B: T.81, Y.82 Chain C: F.5, L.7 1 PLIP interactions: 1 interactions with chain B Water bridges: B:T.81 EDO.9: 4 residues within 4Å: Chain B: S.183, V.184, T.185, S.186 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.183, B:T.185, B:S.186 EDO.10: 4 residues within 4Å: Chain B: S.130, I.131, E.132, E.180 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.130, B:E.132

1 x DHL: 2-AMINO-ETHANETHIOL(Non-covalent)

DHL.11: 3 residues within 4Å: Chain A: S.54, E.56 Chain C: C.3 1 PLIP interactions: 1 interactions with chain A Water bridges: A:E.56

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
A

B
B

C
C

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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