SMTL ID : 8rhq.1

Crystal structure of HLA-A*11:01 in complex with SVLNDIFSRL, an 10-mer epitope from SARS-CoV-2 Spike (S975-984)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

hetero-3-3-3-mer

Ligands

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

EDO.1: 5 residues within 4Å: Chain A: R.30, F.32, Y.51, D.53 Chain B: Y.64 Ligand excluded by PLIP EDO.2: 6 residues within 4Å: Chain A: A.182, Y.183, G.186, R.187 Chain G: N.4 Ligands: EDO.3 Ligand excluded by PLIP EDO.3: 4 residues within 4Å: Chain A: A.182, E.185, G.186 Ligands: EDO.2 Ligand excluded by PLIP EDO.4: 6 residues within 4Å: Chain A: Y.109, D.146, Y.147, D.161, A.163, A.164 Ligand excluded by PLIP EDO.5: 3 residues within 4Å: Chain A: D.146 Chain B: K.59, W.61 Ligand excluded by PLIP EDO.6: 8 residues within 4Å: Chain B: L.41, K.42, N.43, G.44, E.78, Y.79, A.80, K.95 Ligand excluded by PLIP EDO.7: 5 residues within 4Å: Chain A: V.255, R.258, W.268 Chain B: Q.9, M.100 Ligand excluded by PLIP EDO.9: 8 residues within 4Å: Chain C: G.25, H.27, V.127, G.128, P.129, G.131, R.193, L.196 Ligand excluded by PLIP EDO.10: 5 residues within 4Å: Chain C: R.30, F.32, Y.51, D.53, D.54 Ligand excluded by PLIP EDO.11: 4 residues within 4Å: Chain C: P.259, F.265 Chain D: Y.27, Y.64 Ligand excluded by PLIP EDO.12: 1 residues within 4Å: Chain C: P.74 Ligand excluded by PLIP EDO.15: 5 residues within 4Å: Chain C: G.144, K.145 Chain D: I.2, D.60, W.61 Ligand excluded by PLIP EDO.16: 3 residues within 4Å: Chain D: S.58, K.59, D.60 Ligand excluded by PLIP EDO.17: 6 residues within 4Å: Chain C: V.255, R.258 Chain D: Q.9, V.10, V.94, M.100 Ligand excluded by PLIP EDO.19: 5 residues within 4Å: Chain E: R.30, F.32, Y.51, D.53, D.54 Ligand excluded by PLIP EDO.23: 7 residues within 4Å: Chain E: L.230, R.258, Q.266 Chain F: Y.11, S.12, H.14, P.15 Ligand excluded by PLIP EDO.24: 4 residues within 4Å: Chain E: R.45, I.47 Chain F: S.34, L.65 Ligand excluded by PLIP

3 x NA: SODIUM ION(Non-functional Binders)

NA.8: 3 residues within 4Å: Chain B: N.84, H.85, L.88 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.84, B:H.85, B:H.85, B:L.88 NA.22: 2 residues within 4Å: Chain E: G.107, N.110 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:N.110 NA.25: 3 residues within 4Å: Chain F: N.84, H.85, L.88 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:N.84, F:H.85, F:L.88

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.13: 5 residues within 4Å: Chain C: Q.56, R.72, G.261 Chain D: S.53, D.54 5 PLIP interactions: 3 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:R.72, C:G.263, D:D.54, D:D.54 Water bridges: C:G.261

3 x CL: CHLORIDE ION(Non-functional Binders)

CL.14: 7 residues within 4Å: Chain C: T.118, Q.120, A.141, Y.142, D.143, G.144 Chain D: H.32 Ligand excluded by PLIP CL.20: 6 residues within 4Å: Chain E: T.118, Q.120, A.141, Y.142, D.143, G.144 Ligand excluded by PLIP CL.21: 6 residues within 4Å: Chain E: W.157, W.171, E.172, H.175, A.176, A.177 Ligand excluded by PLIP

1 x MG: MAGNESIUM ION(Non-covalent)

MG.18: 3 residues within 4Å: Chain D: N.84, H.85, L.88 3 PLIP interactions: 2 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:H.85, D:L.88, H2O.13

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ahn, Y.M. et al., The impact of SARS-CoV-2 spike mutation on peptide presentation is HLA allomorph-specific. Curr Res Struct Biol (2024)

Release Date

2024-05-15

Peptides

HLA class I histocompatibility antigen: ACE
Beta-2-microglobulin: BDF
Spike protein S2': GHI

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

E
E

B
B

D
D

F
F

G
G

H
H

I
I

HLA class I histocompatibility antigen

Beta-2-microglobulin

Spike protein S2'

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