SMTL ID : 7kxk.1

SARS-CoV-2 spike protein in complex with Fab 15033-7, 2-"up"-1-"down" conformation

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-mer

Ligands

12 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: 3 residues within 4Å: Chain A: N.280, E.281, N.282 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 3 residues within 4Å: Chain A: N.331, Q.580, T.581 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 3 residues within 4Å: Chain A: N.709, I.1130, G.1131 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 2 residues within 4Å: Chain A: N.801, Q.804 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 6 residues within 4Å: Chain B: N.122, A.123, T.124, V.127, M.153, V.171 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 3 residues within 4Å: Chain B: E.132, N.164, N.165 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 4 residues within 4Å: Chain B: N.331, Q.580, T.581, L.582 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:T.581 NAG-NAG.10: 3 residues within 4Å: Chain B: S.708, N.709, N.710 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 5 residues within 4Å: Chain B: N.717, N.919, L.922, N.925, Q.926 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 3 residues within 4Å: Chain B: N.801, S.803, Q.804 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 4 residues within 4Å: Chain C: N.717, T.719, L.922, Q.926 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:L.922 NAG-NAG.15: 3 residues within 4Å: Chain C: N.801, S.803, Q.804 No protein-ligand interaction detected (PLIP)

3 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.4: 4 residues within 4Å: Chain A: N.717, T.719, L.922, Q.926 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Q.926 Hydrogen bonds: A:Q.926 NAG-NAG-BMA.8: 2 residues within 4Å: Chain B: N.280, N.282 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.13: 3 residues within 4Å: Chain C: N.343, L.368, S.371 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:S.371

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

NAG.16: 7 residues within 4Å: Chain A: F.338, G.339, F.342, N.343, V.367, L.368, S.371 Ligand excluded by PLIP NAG.17: 5 residues within 4Å: Chain A: D.614, V.615, N.616, Q.644, R.646 Ligand excluded by PLIP NAG.18: 2 residues within 4Å: Chain A: H.655, N.657 Ligand excluded by PLIP NAG.19: 7 residues within 4Å: Chain A: V.705, A.706, A.713, E.1072, K.1073, N.1074 Chain C: Q.895 Ligand excluded by PLIP NAG.20: 4 residues within 4Å: Chain A: N.1098, T.1100, H.1101, F.1103 Ligand excluded by PLIP NAG.21: 2 residues within 4Å: Chain B: T.307, N.603 Ligand excluded by PLIP NAG.22: 3 residues within 4Å: Chain B: V.656, N.657, N.658 Ligand excluded by PLIP NAG.23: 6 residues within 4Å: Chain A: A.893, Q.895 Chain B: A.706, A.713, E.1072, N.1074 Ligand excluded by PLIP NAG.24: 4 residues within 4Å: Chain B: C.1082, G.1085, C.1126, N.1134 Ligand excluded by PLIP NAG.25: 7 residues within 4Å: Chain C: N.122, A.123, T.124, N.125, V.127, M.153, V.171 Ligand excluded by PLIP NAG.26: 3 residues within 4Å: Chain C: T.108, I.233, N.234 Ligand excluded by PLIP NAG.27: 3 residues within 4Å: Chain C: N.280, E.281, N.282 Ligand excluded by PLIP NAG.28: 3 residues within 4Å: Chain C: P.330, N.331, Q.580 Ligand excluded by PLIP NAG.29: 3 residues within 4Å: Chain C: D.614, N.616, Q.644 Ligand excluded by PLIP NAG.30: 4 residues within 4Å: Chain B: D.796 Chain C: S.708, N.709, N.710 Ligand excluded by PLIP NAG.31: 4 residues within 4Å: Chain C: N.1098, T.1100, H.1101, F.1103 Ligand excluded by PLIP

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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