SMTL ID : 7xmn.1

Structure of SARS-CoV-2 ORF8

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

hetero-2-2-mer

Ligands

2 x GLC- GLC: alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose(Non-covalent)

GLC-GLC.1: 11 residues within 4Å: Chain A: A.63, D.65, R.66, E.111, E.153, P.154, Y.155, F.156, W.230, M.330, W.340 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.65, A:R.66, A:Y.155, A:R.344 GLC-GLC.10: 11 residues within 4Å: Chain C: A.63, D.65, R.66, E.111, E.153, P.154, Y.155, F.156, W.230, M.330, W.340 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:D.65, C:R.66, C:E.153, C:Y.155, C:R.344

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

MES.2: 2 residues within 4Å: Chain A: A.141, K.142 No protein-ligand interaction detected (PLIP) MES.11: 2 residues within 4Å: Chain C: A.141, K.142 No protein-ligand interaction detected (PLIP)

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

SO4.3: 11 residues within 4Å: Chain A: T.345, A.346, N.349, Q.355, A.360, A.363, A.364, N.367 Chain D: S.67, C.68, L.69 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain D Hydrogen bonds: A:T.345, A:N.349, A:Q.355, A:N.367, D:C.68, D:L.69 SO4.4: 3 residues within 4Å: Chain A: P.40, D.41, K.46 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.41 Salt bridges: A:K.46 SO4.5: 4 residues within 4Å: Chain A: F.92, A.324, Q.325, I.329 No protein-ligand interaction detected (PLIP) SO4.8: 3 residues within 4Å: Chain B: R.33, R.86 Ligands: NNH.7 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:R.33, B:R.86 SO4.9: 6 residues within 4Å: Chain A: Q.335 Chain B: H.2, F.26, E.95, Y.96, H.97 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:Y.96, A:Q.335 Salt bridges: B:H.2, B:H.97 SO4.12: 11 residues within 4Å: Chain B: S.67, C.68, L.69 Chain C: T.345, A.346, N.349, Q.355, A.360, A.363, A.364, N.367 6 PLIP interactions: 4 interactions with chain C, 2 interactions with chain B Hydrogen bonds: C:N.349, C:Q.355, C:N.367, B:C.68, B:L.69 Water bridges: C:T.345 SO4.13: 3 residues within 4Å: Chain C: P.40, D.41, K.46 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:D.41 Salt bridges: C:K.46 SO4.14: 4 residues within 4Å: Chain C: F.92, A.324, Q.325, I.329 No protein-ligand interaction detected (PLIP) SO4.17: 3 residues within 4Å: Chain D: R.33, R.86 Ligands: NNH.16 2 PLIP interactions: 2 interactions with chain D Salt bridges: D:R.33, D:R.86 SO4.18: 6 residues within 4Å: Chain C: Q.335 Chain D: H.2, F.26, E.95, Y.96, H.97 5 PLIP interactions: 4 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:E.95, D:Y.96, C:Q.335 Salt bridges: D:H.2, D:H.97

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

NAG.6: 4 residues within 4Å: Chain B: H.13, N.63, N.74, Q.76 No protein-ligand interaction detected (PLIP) NAG.15: 4 residues within 4Å: Chain D: H.13, N.63, N.74, Q.76 No protein-ligand interaction detected (PLIP)

2 x NNH: NOR-N-OMEGA-HYDROXY-L-ARGININE(Non-covalent)

NNH.7: 6 residues within 4Å: Chain A: S.73 Chain B: Y.31, R.86, F.93, Y.96 Ligands: SO4.8 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Y.31, B:Y.31, B:R.86 NNH.16: 6 residues within 4Å: Chain C: S.73 Chain D: Y.31, R.86, F.93, Y.96 Ligands: SO4.17 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:Y.31, D:Y.31, D:Y.31, D:R.86

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wu, F. et al., Glycosylated, Lipid-Binding, CDR-Like Domains of SARS-CoV-2 ORF8 Indicate Unique Sites of Immune Regulation. Microbiol Spectr (2023)

Release Date

2023-05-31

Peptides

Maltodextrin-binding protein: AC
ORF8 protein: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
A

B
B

D
B

Maltodextrin-binding protein

ORF8 protein