SMTL ID : 8cmh.1

Human Leukocyte Antigen class II allotype DR1 presenting SARS-CoV-2 Omicron (BA.1) Spike peptide S486-505

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.64 Å

Oligo State

hetero-1-1-1-mer

Ligands

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

EDO.1: 3 residues within 4Å: Chain A: V.117, V.118, F.138 Ligand excluded by PLIP EDO.2: 3 residues within 4Å: Chain A: K.112, R.141, R.147 Ligand excluded by PLIP EDO.3: 4 residues within 4Å: Chain A: F.55, E.56 Ligands: EDO.6, DHL.32 Ligand excluded by PLIP EDO.4: 4 residues within 4Å: Chain A: P.174, L.175, L.176, K.177 Ligand excluded by PLIP EDO.5: 4 residues within 4Å: Chain A: R.124, F.154, L.155, Y.162 Ligand excluded by PLIP EDO.6: 4 residues within 4Å: Chain A: W.44, S.54, F.55 Ligands: EDO.3 Ligand excluded by PLIP EDO.7: 4 residues within 4Å: Chain A: R.141, E.142, D.143 Ligands: EDO.9 Ligand excluded by PLIP EDO.8: 4 residues within 4Å: Chain A: V.86, P.87, E.89, K.112 Ligand excluded by PLIP EDO.9: 7 residues within 4Å: Chain A: I.9, D.26, G.29, P.140, R.141, E.142 Ligands: EDO.7 Ligand excluded by PLIP EDO.10: 4 residues within 4Å: Chain A: N.95, V.105, Y.151 Chain B: D.156 Ligand excluded by PLIP EDO.11: 6 residues within 4Å: Chain A: V.118, N.119, V.120, E.135, H.150 Ligands: EDO.13 Ligand excluded by PLIP EDO.12: 3 residues within 4Å: Chain A: P.103, P.153, F.154 Ligand excluded by PLIP EDO.13: 7 residues within 4Å: Chain A: V.120, W.122, V.133, S.134, E.135, H.150 Ligands: EDO.11 Ligand excluded by PLIP EDO.14: 4 residues within 4Å: Chain A: E.135, T.136, V.137, F.138 Ligand excluded by PLIP EDO.15: 2 residues within 4Å: Chain A: N.16, P.17 Ligand excluded by PLIP EDO.16: 4 residues within 4Å: Chain A: R.45, S.134, E.135, Y.151 Ligand excluded by PLIP EDO.17: 1 residues within 4Å: Chain A: K.76 Ligand excluded by PLIP EDO.19: 2 residues within 4Å: Chain B: V.147, S.148 Ligand excluded by PLIP EDO.20: 4 residues within 4Å: Chain B: K.102, V.103, L.188, V.190 Ligand excluded by PLIP EDO.21: 5 residues within 4Å: Chain B: E.26, R.27, V.28, V.79, R.84 Ligand excluded by PLIP EDO.22: 6 residues within 4Å: Chain B: S.130, I.131, E.132, E.180, H.181, P.182 Ligand excluded by PLIP EDO.23: 1 residues within 4Å: Chain B: R.193 Ligand excluded by PLIP EDO.24: 6 residues within 4Å: Chain B: E.180, H.181, V.184, T.185, S.186, P.187 Ligand excluded by PLIP EDO.25: 2 residues within 4Å: Chain B: V.190, E.191 Ligand excluded by PLIP EDO.26: 5 residues within 4Å: Chain B: A.53, V.54, T.55, E.56, R.59 Ligand excluded by PLIP EDO.27: 3 residues within 4Å: Chain B: G.145, L.165, E.166 Ligand excluded by PLIP EDO.28: 4 residues within 4Å: Chain B: E.141, E.142, K.143, A.144 Ligand excluded by PLIP EDO.29: 3 residues within 4Å: Chain B: T.81, Y.82 Chain C: L.7 Ligand excluded by PLIP EDO.30: 3 residues within 4Å: Chain B: I.131, S.148, T.161 Ligand excluded by PLIP EDO.31: 3 residues within 4Å: Chain B: K.69, L.72, R.76 Ligand excluded by PLIP

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

SO4.18: 2 residues within 4Å: Chain A: R.124, N.125 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.125 Water bridges: A:R.124, A:R.124 Salt bridges: A:R.124, A:K.127

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

DHL.32: 4 residues within 4Å: Chain A: S.54 Chain C: C.3, Y.4 Ligands: EDO.3 No protein-ligand interaction detected (PLIP)

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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