SMTL ID : 7ru3.1

CC6.33 IgG in complex with SARS-CoV-2-6P-Mut7 S protein (non-uniform refinement)

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-2-3-mer

Ligands

5 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: 9 residues within 4Å: Chain A: Q.1, D.103, L.105, Y.107 Chain B: Y.50, S.54, T.57 Chain C: N.343, A.344 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 3 residues within 4Å: Chain C: N.717, L.922, Q.926 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:L.922 NAG-NAG.4: 3 residues within 4Å: Chain E: N.717, L.922, Q.926 1 PLIP interactions: 1 interactions with chain E Hydrophobic interactions: E:L.922 NAG-NAG.5: 3 residues within 4Å: Chain E: N.801, S.803, Q.804 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 4 residues within 4Å: Chain E: N.1098, T.1100, H.1101, F.1103 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- FUC: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-FUC.3: 12 residues within 4Å: Chain E: N.343, A.344, S.371, S.373, W.436, N.440 Chain F: Q.1, W.102, D.103, L.105 Chain G: S.54, T.57 4 PLIP interactions: 1 interactions with chain F, 3 interactions with chain E Hydrophobic interactions: F:L.105 Hydrogen bonds: E:N.440, E:S.371, E:S.371, E:S.373

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

NAG.7: 4 residues within 4Å: Chain C: C.15, V.16, N.17, N.137 Ligand excluded by PLIP NAG.8: 2 residues within 4Å: Chain C: Y.28, N.61 Ligand excluded by PLIP NAG.9: 5 residues within 4Å: Chain C: N.122, T.124, N.125, V.127, V.171 Ligand excluded by PLIP NAG.10: 3 residues within 4Å: Chain C: N.164, N.165 Chain E: Y.351 Ligand excluded by PLIP NAG.11: 5 residues within 4Å: Chain C: N.234 Chain E: R.457, S.459, K.462, E.465 Ligand excluded by PLIP NAG.12: 3 residues within 4Å: Chain C: N.280, E.281, N.282 Ligand excluded by PLIP NAG.13: 2 residues within 4Å: Chain C: N.331, Q.580 Ligand excluded by PLIP NAG.14: 4 residues within 4Å: Chain C: N.616, C.617, T.618, Q.644 Ligand excluded by PLIP NAG.15: 1 residues within 4Å: Chain C: N.657 Ligand excluded by PLIP NAG.16: 3 residues within 4Å: Chain C: N.709, N.710, G.1131 Ligand excluded by PLIP NAG.17: 2 residues within 4Å: Chain C: N.801, S.803 Ligand excluded by PLIP NAG.18: 3 residues within 4Å: Chain C: A.706, N.1074 Chain D: Q.895 Ligand excluded by PLIP NAG.19: 3 residues within 4Å: Chain C: N.1098, T.1100, F.1103 Ligand excluded by PLIP NAG.20: 1 residues within 4Å: Chain C: N.1134 Ligand excluded by PLIP NAG.21: 4 residues within 4Å: Chain D: C.15, N.17, C.136, N.137 Ligand excluded by PLIP NAG.22: 2 residues within 4Å: Chain D: N.234, T.236 Ligand excluded by PLIP NAG.23: 3 residues within 4Å: Chain D: N.331, Q.580, T.581 Ligand excluded by PLIP NAG.24: 3 residues within 4Å: Chain D: N.616, T.618, Q.644 Ligand excluded by PLIP NAG.25: 4 residues within 4Å: Chain D: N.709, N.710, G.1131 Chain E: D.796 Ligand excluded by PLIP NAG.26: 1 residues within 4Å: Chain D: N.717 Ligand excluded by PLIP NAG.27: 3 residues within 4Å: Chain D: K.795, N.801, S.803 Ligand excluded by PLIP NAG.28: 2 residues within 4Å: Chain D: N.1074 Chain E: Q.895 Ligand excluded by PLIP NAG.29: 4 residues within 4Å: Chain D: N.1098, G.1099, T.1100, F.1103 Ligand excluded by PLIP NAG.30: 1 residues within 4Å: Chain D: N.1134 Ligand excluded by PLIP NAG.31: 2 residues within 4Å: Chain E: N.331, Q.580 Ligand excluded by PLIP NAG.32: 1 residues within 4Å: Chain E: N.616 Ligand excluded by PLIP NAG.33: 3 residues within 4Å: Chain E: N.709, N.710, G.1131 Ligand excluded by PLIP NAG.34: 2 residues within 4Å: Chain E: S.711, N.1074 Ligand excluded by PLIP NAG.35: 2 residues within 4Å: Chain E: I.1132, N.1134 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhao, F. et al., Engineering SARS-CoV-2 neutralizing antibodies for increased potency and reduced viral escape pathways. Iscience (2022)

Release Date

2022-08-24

Peptides

CC6.33 IgG heavy chain Fv: AF
CC6.33 IgG Kappa chain Fv: BG
Spike glycoprotein: CDE

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
H

F
E

B
L

G
F

C
A

D
C

E
B

CC6.33 IgG heavy chain Fv

CC6.33 IgG Kappa chain Fv

Spike glycoprotein

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