SMTL ID : 7sn3.1

Structure of human SARS-CoV-2 spike glycoprotein trimer bound by neutralizing antibody C1C-A3 Fab (variable region)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-mer

Ligands

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.1: 7 residues within 4Å: Chain A: F.338, G.339, F.342, N.343, V.367 Chain E: N.115, W.116 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:N.115 NAG-NAG-BMA.2: 6 residues within 4Å: Chain B: F.338, F.342, N.343, V.367, L.368 Chain G: W.116 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.3: 7 residues within 4Å: Chain C: F.338, F.342, N.343, V.367, L.368 Chain I: N.115, W.116 1 PLIP interactions: 1 interactions with chain I Hydrogen bonds: I:N.115

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

NAG.4: 2 residues within 4Å: Chain A: Y.28, N.61 Ligand excluded by PLIP NAG.5: 4 residues within 4Å: Chain A: N.122, A.123, T.124, V.127 Ligand excluded by PLIP NAG.6: 1 residues within 4Å: Chain A: N.234 Ligand excluded by PLIP NAG.7: 2 residues within 4Å: Chain A: E.281, N.282 Ligand excluded by PLIP NAG.8: 2 residues within 4Å: Chain A: N.331, Q.580 Ligand excluded by PLIP NAG.9: 2 residues within 4Å: Chain A: N.603, T.604 Ligand excluded by PLIP NAG.10: 2 residues within 4Å: Chain A: N.616, T.618 Ligand excluded by PLIP NAG.11: 1 residues within 4Å: Chain A: N.657 Ligand excluded by PLIP NAG.12: 2 residues within 4Å: Chain A: N.709, G.1131 Ligand excluded by PLIP NAG.13: 3 residues within 4Å: Chain A: N.717, Q.926, Q.1071 Ligand excluded by PLIP NAG.14: 3 residues within 4Å: Chain A: N.801, S.803, Q.804 Ligand excluded by PLIP NAG.15: 3 residues within 4Å: Chain A: A.706, E.1072, N.1074 Ligand excluded by PLIP NAG.16: 3 residues within 4Å: Chain A: N.1098, H.1101, F.1103 Ligand excluded by PLIP NAG.17: 1 residues within 4Å: Chain A: N.1134 Ligand excluded by PLIP NAG.18: 2 residues within 4Å: Chain A: Q.115, N.165 Ligand excluded by PLIP NAG.19: 2 residues within 4Å: Chain B: Y.28, N.61 Ligand excluded by PLIP NAG.20: 5 residues within 4Å: Chain B: N.121, N.122, V.126, F.192, L.226 Ligand excluded by PLIP NAG.21: 1 residues within 4Å: Chain B: N.234 Ligand excluded by PLIP NAG.22: 2 residues within 4Å: Chain B: E.281, N.282 Ligand excluded by PLIP NAG.23: 4 residues within 4Å: Chain B: N.331, P.579, Q.580, L.582 Ligand excluded by PLIP NAG.24: 1 residues within 4Å: Chain B: N.603 Ligand excluded by PLIP NAG.25: 2 residues within 4Å: Chain B: N.616, T.618 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.709, G.1131 Ligand excluded by PLIP NAG.28: 3 residues within 4Å: Chain B: N.717, Q.926, Q.1071 Ligand excluded by PLIP NAG.29: 3 residues within 4Å: Chain B: N.801, S.803, Q.804 Ligand excluded by PLIP NAG.30: 3 residues within 4Å: Chain B: A.706, E.1072, N.1074 Ligand excluded by PLIP NAG.31: 3 residues within 4Å: Chain B: N.1098, H.1101, F.1103 Ligand excluded by PLIP NAG.32: 1 residues within 4Å: Chain B: N.1134 Ligand excluded by PLIP NAG.33: 3 residues within 4Å: Chain B: Q.115, N.165, T.167 Ligand excluded by PLIP NAG.34: 1 residues within 4Å: Chain C: N.61 Ligand excluded by PLIP NAG.35: 2 residues within 4Å: Chain C: N.122, V.127 Ligand excluded by PLIP NAG.36: 1 residues within 4Å: Chain C: N.234 Ligand excluded by PLIP NAG.37: 1 residues within 4Å: Chain C: N.282 Ligand excluded by PLIP NAG.38: 3 residues within 4Å: Chain C: N.331, P.579, Q.580 Ligand excluded by PLIP NAG.39: 1 residues within 4Å: Chain C: N.603 Ligand excluded by PLIP NAG.40: 2 residues within 4Å: Chain C: N.616, T.618 Ligand excluded by PLIP NAG.41: 1 residues within 4Å: Chain C: N.657 Ligand excluded by PLIP NAG.42: 2 residues within 4Å: Chain C: N.709, G.1131 Ligand excluded by PLIP NAG.43: 3 residues within 4Å: Chain C: N.717, Q.926, Q.1071 Ligand excluded by PLIP NAG.44: 3 residues within 4Å: Chain C: N.801, S.803, Q.804 Ligand excluded by PLIP NAG.45: 3 residues within 4Å: Chain C: A.706, E.1072, N.1074 Ligand excluded by PLIP NAG.46: 3 residues within 4Å: Chain C: N.1098, H.1101, F.1103 Ligand excluded by PLIP NAG.47: 2 residues within 4Å: Chain C: C.1082, N.1134 Ligand excluded by PLIP NAG.48: 4 residues within 4Å: Chain C: Q.115, N.165, C.166, T.167 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nabel, K.G. et al., Structural basis for continued antibody evasion by the SARS-CoV-2 receptor binding domain. Science (2022)

Release Date

2021-12-08

Peptides

Spike glycoprotein: ABC
neutralizing antibody C1C-A3 heavy chain variable region: DFH
neutralizing antibody C1C-A3 light chain variable region: EGI

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

F
F

H
H

E
E

G
G

I
L

Spike glycoprotein

neutralizing antibody C1C-A3 heavy chain variable region

neutralizing antibody C1C-A3 light chain variable region

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