SMTL ID : 8euq.2 (1 other biounit)

Crystal structure of HLA-DRA*01:01/HLA-DRB1*04:01 in complex with c44H10 Fab

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.09 Å

Oligo State

hetero-1-1-1-1-mer

Ligands

1 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.1: 7 residues within 4Å: Chain A: V.114, N.116, E.164, H.165, W.166 Chain C: D.29, T.30 No protein-ligand interaction detected (PLIP)

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

SO4.2: 3 residues within 4Å: Chain A: D.108, K.109, R.138 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:K.109, A:R.138 SO4.3: 2 residues within 4Å: Chain B: R.18 Chain C: R.82 1 PLIP interactions: 1 interactions with chain C Salt bridges: C:R.82 SO4.4: 3 residues within 4Å: Chain A: R.42, Y.148 Chain C: D.179 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.42 SO4.5: 3 residues within 4Å: Chain C: T.30, R.31, R.33 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:R.31 Salt bridges: C:R.33 SO4.6: 3 residues within 4Å: Chain B: K.60 Chain C: R.52, R.66 2 PLIP interactions: 2 interactions with chain C Salt bridges: C:R.52, C:R.66 SO4.8: 5 residues within 4Å: Chain A: K.109 Chain D: V.2, Y.32, R.97, Y.109 5 PLIP interactions: 4 interactions with chain D, 1 interactions with chain A Hydrogen bonds: D:Y.32, D:Y.32, D:Y.109 Salt bridges: D:R.97, A:K.109

1 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.7: 2 residues within 4Å: Chain C: N.46, E.49 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:N.46, C:E.49

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kassardjian, A. et al., Modular adjuvant-free pan-HLA-DR-immunotargeting subunit vaccine against SARS-CoV-2 elicits broad sarbecovirus-neutralizing antibody responses. Cell Rep (2023)

Release Date

2023-04-19

Peptides

HLA class II histocompatibility antigen, DR alpha chain: A
c44H10 Fab light chain: B
Hemagglutinin HA1 chain,HLA class II histocompatibility antigen DR beta chain: C
c44H10 Fab heavy chain: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
F

B
H

C
G

D
I

HLA class II histocompatibility antigen, DR alpha chain

c44H10 Fab light chain

Hemagglutinin HA1 chain,HLA class II histocompatibility antigen DR beta chain

c44H10 Fab heavy chain

Related Entries With Identical Sequence