SMTL ID : 8cmg.1

Human Leukocyte Antigen class II allotype DR1 presenting SARS-CoV-2 nsp14 peptide (orf1ab)6420-6434

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.64 Å

Oligo State

hetero-1-1-1-mer

Ligands

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

EDO.1: 4 residues within 4Å: Chain A: T.42, W.44, S.54, F.55 Ligand excluded by PLIP EDO.2: 7 residues within 4Å: Chain A: I.9, D.26, G.29, P.140, R.141, E.142, R.147 Ligand excluded by PLIP EDO.3: 4 residues within 4Å: Chain A: R.45, Y.151 Chain B: D.156 Ligands: EDO.5 Ligand excluded by PLIP EDO.4: 4 residues within 4Å: Chain A: V.117, E.167, H.168, W.169 Ligand excluded by PLIP EDO.5: 6 residues within 4Å: Chain A: N.95, I.107, Y.151 Chain B: N.154, D.156 Ligands: EDO.3 Ligand excluded by PLIP EDO.6: 4 residues within 4Å: Chain A: Q.19, S.20, G.21, M.37 Ligand excluded by PLIP EDO.7: 6 residues within 4Å: Chain A: I.83, N.85, W.169 Chain B: T.7, R.8, R.10 Ligand excluded by PLIP EDO.8: 3 residues within 4Å: Chain A: E.56, G.59 Ligands: EDO.20 Ligand excluded by PLIP EDO.11: 3 residues within 4Å: Chain B: S.148, T.161, V.163 Ligand excluded by PLIP EDO.12: 7 residues within 4Å: Chain B: Q.74, T.81, Y.82 Chain C: N.5, M.6, M.7 Ligands: EDO.20 Ligand excluded by PLIP EDO.13: 5 residues within 4Å: Chain B: E.26, R.27, V.28, V.79, R.84 Ligand excluded by PLIP EDO.14: 2 residues within 4Å: Chain B: S.46, D.47 Ligand excluded by PLIP EDO.15: 5 residues within 4Å: Chain A: F.109, F.149 Chain B: L.151, I.152, Q.153 Ligand excluded by PLIP EDO.16: 3 residues within 4Å: Chain B: D.70, E.73, Q.74 Ligand excluded by PLIP EDO.17: 4 residues within 4Å: Chain A: E.142 Chain B: E.18, H.20, R.33 Ligand excluded by PLIP EDO.20: 4 residues within 4Å: Chain C: N.5, M.6 Ligands: EDO.8, EDO.12 Ligand excluded by PLIP

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

SO4.9: 2 residues within 4Å: Chain A: K.112, R.141 3 PLIP interactions: 3 interactions with chain A Water bridges: A:R.141 Salt bridges: A:K.112, A:R.141 SO4.10: 3 residues within 4Å: Chain A: R.124, N.125, K.127 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.125 Salt bridges: A:R.124, A:K.127 SO4.18: 5 residues within 4Å: Chain B: A.53, V.54, T.55, E.56, R.59 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.56 Water bridges: B:E.56 Salt bridges: B:R.59 SO4.19: 2 residues within 4Å: Chain B: K.69, R.76 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:K.69, 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
Non-structural protein 7: 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)

Non-structural protein 7

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