SMTL ID : 7kxj.1

SARS-CoV-2 spike protein in complex with Fab 15033-7, 3-"up", asymmetric

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-mer

Ligands

2 x NAG- NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA.1: 4 residues within 4Å: Chain A: N.331, T.333, Q.580, T.581 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.2: 4 residues within 4Å: Chain B: R.328, N.331, Q.580, T.581 No protein-ligand interaction detected (PLIP)

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.3: 8 residues within 4Å: Chain B: N.334, F.338, G.339, F.342, N.343, V.367, L.368, S.371 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.334, B:N.334, B:S.371

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

NAG.4: 4 residues within 4Å: Chain A: N.282 Chain B: K.558, F.559, L.560 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:L.560 NAG.5: 5 residues within 4Å: Chain A: F.342, N.343, L.368, S.371, S.373 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.342 Hydrogen bonds: A:S.371, A:S.371, A:S.373 NAG.6: 7 residues within 4Å: Chain B: A.27, Y.28, T.29, N.30, F.59, S.60, N.61 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Y.28, B:T.29, B:N.61 NAG.7: 4 residues within 4Å: Chain B: S.591, D.614, N.616, E.619 No protein-ligand interaction detected (PLIP) NAG.8: 3 residues within 4Å: Chain C: C.15, N.17, N.137 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.137 NAG.9: 5 residues within 4Å: Chain C: A.27, Y.28, T.29, N.61, T.63 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:Y.28, C:T.29 NAG.10: 3 residues within 4Å: Chain A: K.558, L.560 Chain C: N.282 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain C Hydrophobic interactions: A:L.560 Hydrogen bonds: C:N.282

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Miersch, S. et al., Tetravalent SARS-CoV-2 Neutralizing Antibodies Show Enhanced Potency and Resistance to Escape Mutations. J.Mol.Biol. (2021)

Release Date

2021-02-03

Peptides

Spike glycoprotein: ABC
Fab 15033-7 light chain: DFH
Fab 15033-7 heavy chain: EGI

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
L

F
M

H
N

E
H

G
I

I
J

Spike glycoprotein

Fab 15033-7 light chain

Fab 15033-7 heavy chain

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