SMTL ID : 8cmc.1

Human Leukocyte Antigen class II allotype DR1 presenting SARS-CoV-2 Spike peptide S511-530

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.42 Å

Oligo State

hetero-1-1-1-mer

Ligands

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

EDO.1: 4 residues within 4Å: Chain A: T.42, W.44, S.54, F.55 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: 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 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.26, A:R.147 EDO.3: 4 residues within 4Å: Chain A: R.45, Y.151 Chain B: D.156 Ligands: EDO.5 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.45, A:R.45 EDO.4: 4 residues within 4Å: Chain A: V.117, E.167, H.168, W.169 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:V.117, A:W.169 Water bridges: A:H.168 EDO.5: 7 residues within 4Å: Chain A: N.95, V.105, I.107, Y.151 Chain B: N.154, D.156 Ligands: EDO.3 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.156 EDO.6: 6 residues within 4Å: Chain A: I.83, N.85, W.169 Chain B: T.7, R.8, R.10 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:N.85, B:R.10 EDO.7: 3 residues within 4Å: Chain A: R.141, E.142, D.143 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.142, A:D.143 EDO.10: 5 residues within 4Å: Chain B: A.53, V.54, T.55, E.56, R.59 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.56, B:E.56, B:R.59 Water bridges: B:E.56 EDO.11: 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.12: 4 residues within 4Å: Chain A: F.109 Chain B: L.151, I.152, Q.153 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.153 Water bridges: B:L.151 EDO.13: 3 residues within 4Å: Chain B: P.101, K.102, V.103 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:P.101, B:V.103 EDO.14: 2 residues within 4Å: Chain B: S.46, D.47 1 PLIP interactions: 1 interactions with chain B Water bridges: B:S.46 EDO.15: 2 residues within 4Å: Chain B: V.184, T.185 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:T.185 EDO.16: 6 residues within 4Å: Chain B: S.130, I.131, E.132, E.180, H.181, P.182 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.130 EDO.17: 1 residues within 4Å: Chain B: H.115 No protein-ligand interaction detected (PLIP)

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

SO4.8: 2 residues within 4Å: Chain A: K.112, R.141 5 PLIP interactions: 5 interactions with chain A Water bridges: A:K.112, A:R.141, A:D.143 Salt bridges: A:K.112, A:R.141 SO4.9: 3 residues within 4Å: Chain A: R.124, N.125, K.127 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.125 Salt bridges: A:K.127

1 x MES: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID(Non-covalent)

MES.18: 8 residues within 4Å: Chain B: G.129, S.130, I.131, S.148, G.150, L.151, T.161, V.163 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:I.131, B:S.148, B:T.161 Water bridges: B:V.133

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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