SMTL ID : 7u0q.1

SARS-Cov2 S protein structure in complex with neutralizing monoclonal antibody 002-02

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-2-2-mer

Ligands

14 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: 2 residues within 4Å: Chain A: N.331, Q.580 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 1 residues within 4Å: Chain A: N.1134 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 3 residues within 4Å: Chain A: N.1098, H.1101, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 4 residues within 4Å: Chain A: N.717, L.922, Q.926, Q.1071 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 3 residues within 4Å: Chain A: N.709, G.1131 Chain B: D.796 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 6 residues within 4Å: Chain A: F.338, G.339, F.342, N.343, V.367, S.371 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:V.367 NAG-NAG.7: 1 residues within 4Å: Chain B: N.1134 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 4 residues within 4Å: Chain B: N.1098, T.1100, H.1101, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 5 residues within 4Å: Chain B: N.717, T.719, L.922, Q.926, Q.1071 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 4 residues within 4Å: Chain B: K.795, N.801, S.803, Q.804 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 1 residues within 4Å: Chain C: N.1134 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 4 residues within 4Å: Chain C: N.1098, T.1100, H.1101, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 3 residues within 4Å: Chain C: N.717, L.922, Q.1071 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 5 residues within 4Å: Chain C: F.338, G.339, F.342, N.343, V.367 No protein-ligand interaction detected (PLIP)

1 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.15: 2 residues within 4Å: Chain C: N.331, Q.580 No protein-ligand interaction detected (PLIP)

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

NAG.16: 2 residues within 4Å: Chain A: N.280, N.282 Ligand excluded by PLIP NAG.17: 1 residues within 4Å: Chain A: N.657 Ligand excluded by PLIP NAG.18: 2 residues within 4Å: Chain A: N.616, T.618 Ligand excluded by PLIP NAG.19: 2 residues within 4Å: Chain A: N.801, S.803 Ligand excluded by PLIP NAG.20: 2 residues within 4Å: Chain A: E.1072, N.1074 Ligand excluded by PLIP NAG.21: 1 residues within 4Å: Chain A: N.61 Ligand excluded by PLIP NAG.22: 2 residues within 4Å: Chain A: Q.115, N.234 Ligand excluded by PLIP NAG.23: 4 residues within 4Å: Chain A: Q.115, E.132, N.165, T.167 Ligand excluded by PLIP NAG.24: 2 residues within 4Å: Chain A: N.603, T.604 Ligand excluded by PLIP NAG.25: 2 residues within 4Å: Chain B: E.281, N.282 Ligand excluded by PLIP NAG.26: 2 residues within 4Å: Chain B: H.655, N.657 Ligand excluded by PLIP NAG.27: 2 residues within 4Å: Chain B: N.616, T.618 Ligand excluded by PLIP NAG.28: 2 residues within 4Å: Chain B: N.709, G.1131 Ligand excluded by PLIP NAG.29: 1 residues within 4Å: Chain B: N.1074 Ligand excluded by PLIP NAG.30: 2 residues within 4Å: Chain B: E.309, N.603 Ligand excluded by PLIP NAG.31: 1 residues within 4Å: Chain B: N.17 Ligand excluded by PLIP NAG.32: 3 residues within 4Å: Chain C: N.280, E.281, N.282 Ligand excluded by PLIP NAG.33: 1 residues within 4Å: Chain C: N.657 Ligand excluded by PLIP NAG.34: 2 residues within 4Å: Chain C: N.616, T.618 Ligand excluded by PLIP NAG.35: 2 residues within 4Å: Chain C: N.709, G.1131 Ligand excluded by PLIP NAG.36: 1 residues within 4Å: Chain C: N.1074 Ligand excluded by PLIP NAG.37: 1 residues within 4Å: Chain C: N.603 Ligand excluded by PLIP NAG.38: 2 residues within 4Å: Chain C: E.132, N.165 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Patel, A. et al., Molecular basis of SARS-CoV-2 Omicron variant evasion from shared neutralizing antibody response. Structure (2023)

Release Date

2023-03-01

Peptides

Spike glycoprotein: ABC
mAb 002-02 light chain: DF
mAb 002-02 Heavy chain: EG

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
F

F
I

E
G

G
J

Spike glycoprotein

mAb 002-02 light chain

mAb 002-02 Heavy chain

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