SMTL ID : 9gvo.1

type-I interferons autoantibodies pmab15 and pmab14 in complex with Interferon alpha-2

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.81 Å

Oligo State

hetero-1-1-1-mer

Ligands

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 4 residues within 4Å: Chain A: F.29, T.30, H.34, K.100 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.30, A:T.30, A:T.30, A:K.100, A:K.100 GOL.2: 7 residues within 4Å: Chain A: T.238 Chain B: G.37, F.38, Q.40, E.41 Chain C: R.174 Ligands: GOL.3 6 PLIP interactions: 2 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:Q.40, A:T.238, A:T.238 Water bridges: B:G.37, A:T.238, A:T.238 GOL.3: 5 residues within 4Å: Chain B: D.35, G.37, F.38, Q.40 Ligands: GOL.2 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:D.35, B:G.37, B:F.38, B:F.38 Water bridges: B:D.35, B:F.36, B:E.146, B:E.146, B:R.149 GOL.4: 4 residues within 4Å: Chain B: Q.61, F.64, Y.89, L.92 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.61, B:Y.89 Water bridges: B:N.65 GOL.5: 4 residues within 4Å: Chain B: I.24, S.28, P.137, C.138 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.28 Water bridges: B:S.28, B:C.138 GOL.8: 3 residues within 4Å: Chain C: Y.107, D.109, Y.196 7 PLIP interactions: 7 interactions with chain C Water bridges: C:G.104, C:D.109, C:D.109, C:Y.179, C:Y.196, C:Y.196, C:S.200

2 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.6: 4 residues within 4Å: Chain A: Q.171, S.172 Chain B: H.34, K.133 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Salt bridges: B:H.34, B:K.133 Hydrogen bonds: A:S.172 PO4.9: 5 residues within 4Å: Chain C: R.186, R.192, P.206, R.208, E.228 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:E.228 Water bridges: C:R.192 Salt bridges: C:R.186, C:R.192, C:R.208

1 x K: POTASSIUM ION(Non-covalent)

K.7: 1 residues within 4Å: Chain C: S.176 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Vanderkerken, M. et al., Temporal and structural insights into type-I interferons autoantibodies in severe COVID-19. To Be Published

Release Date

2025-10-08

Peptides

scFv type-I interferons autoantibody pmab14: A
Interferon alpha-2: B
scFv type-I interferons autoantibody pmab15: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
H

scFv type-I interferons autoantibody pmab14

Interferon alpha-2

scFv type-I interferons autoantibody pmab15

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