SMTL ID : 7u0x.1

SARS-Cov2 S protein structure in complex with neutralizing monoclonal antibody 002-13

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-2-2-mer

Ligands

15 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.331, Q.580, L.582 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: 2 residues within 4Å: Chain A: N.1098, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 5 residues within 4Å: Chain A: N.717, L.922, N.925, Q.926, Q.1071 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.925 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: 3 residues within 4Å: Chain A: C.15, N.17, N.137 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 1 residues within 4Å: Chain B: N.1134 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 3 residues within 4Å: Chain B: N.1098, T.1100, H.1101 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 4 residues within 4Å: Chain B: N.717, T.719, L.922, Q.926 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 3 residues within 4Å: Chain B: N.801, S.803, Q.804 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 3 residues within 4Å: Chain B: N.331, Q.580, T.581 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 1 residues within 4Å: Chain C: N.1134 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 3 residues within 4Å: Chain C: N.1098, H.1101, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 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.15: 2 residues within 4Å: Chain C: N.801, S.803 No protein-ligand interaction detected (PLIP)

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

NAG.16: 2 residues within 4Å: Chain A: E.281, 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: N.1074 Chain B: Q.895 Ligand excluded by PLIP NAG.21: 1 residues within 4Å: Chain A: N.61 Ligand excluded by PLIP NAG.22: 3 residues within 4Å: Chain A: G.232, I.233, N.234 Ligand excluded by PLIP NAG.23: 2 residues within 4Å: Chain A: Q.115, N.165 Ligand excluded by PLIP NAG.24: 1 residues within 4Å: Chain A: N.603 Ligand excluded by PLIP NAG.25: 3 residues within 4Å: Chain A: G.339, F.342, N.343 Ligand excluded by PLIP NAG.26: 1 residues within 4Å: Chain B: N.282 Ligand excluded by PLIP NAG.27: 1 residues within 4Å: Chain B: N.657 Ligand excluded by PLIP NAG.28: 1 residues within 4Å: Chain B: N.616 Ligand excluded by PLIP NAG.29: 3 residues within 4Å: Chain B: N.709, G.1131 Chain C: D.796 Ligand excluded by PLIP NAG.30: 3 residues within 4Å: Chain B: E.1072, N.1074 Chain C: Q.895 Ligand excluded by PLIP NAG.31: 2 residues within 4Å: Chain B: N.603, T.604 Ligand excluded by PLIP NAG.32: 3 residues within 4Å: Chain B: N.17, T.19, N.137 Ligand excluded by PLIP NAG.33: 4 residues within 4Å: Chain B: F.338, G.339, F.342, N.343 Ligand excluded by PLIP NAG.34: 1 residues within 4Å: Chain C: N.282 Ligand excluded by PLIP NAG.35: 1 residues within 4Å: Chain C: N.657 Ligand excluded by PLIP NAG.36: 3 residues within 4Å: Chain C: N.616, T.618, Q.644 Ligand excluded by PLIP NAG.37: 3 residues within 4Å: Chain A: D.796 Chain C: N.709, G.1131 Ligand excluded by PLIP NAG.38: 2 residues within 4Å: Chain C: A.706, N.1074 Ligand excluded by PLIP NAG.39: 3 residues within 4Å: Chain C: Y.28, N.61, R.634 Ligand excluded by PLIP NAG.40: 1 residues within 4Å: Chain C: N.234 Ligand excluded by PLIP NAG.41: 1 residues within 4Å: Chain C: N.603 Ligand excluded by PLIP NAG.42: 3 residues within 4Å: Chain C: Q.115, E.132, N.165 Ligand excluded by PLIP NAG.43: 2 residues within 4Å: Chain C: N.17, N.137 Ligand excluded by PLIP NAG.44: 2 residues within 4Å: Chain C: F.342, N.343 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 002-13 heavy chain: DF
mAb 002-13 Light chain: EG

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
F

F
H

E
G

G
L

Spike glycoprotein

mAb 002-13 heavy chain

mAb 002-13 Light chain

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