SMTL ID : 7lrt.1

Cryo-EM structure of SARS-CoV-2 spike in complex with neutralizing antibody A23-58.1 that targets the receptor-binding domain

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-mer

Ligands

4 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: 4 residues within 4Å: Chain A: N.100, S.102, D.111 Chain B: T.57 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.2: 4 residues within 4Å: Chain C: M.2, N.100, D.111 Chain D: T.57 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.3: 5 residues within 4Å: Chain E: M.2, N.100, S.102, D.111 Chain F: T.57 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.17: 2 residues within 4Å: Chain I: N.318, Q.567 No protein-ligand interaction detected (PLIP)

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.4: 3 residues within 4Å: Chain G: N.318, P.566, Q.567 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 1 residues within 4Å: Chain G: N.1121 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 3 residues within 4Å: Chain G: N.1085, T.1087, H.1088 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 2 residues within 4Å: Chain G: N.704, L.909 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 1 residues within 4Å: Chain G: N.696 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 3 residues within 4Å: Chain G: C.2, N.4, N.124 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 1 residues within 4Å: Chain H: N.1121 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 3 residues within 4Å: Chain H: N.1085, T.1087, H.1088 1 PLIP interactions: 1 interactions with chain H Hydrogen bonds: H:H.1088 NAG-NAG.13: 2 residues within 4Å: Chain H: N.704, Q.1058 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 3 residues within 4Å: Chain H: N.788, S.790, Q.791 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 2 residues within 4Å: Chain H: N.318, Q.567 No protein-ligand interaction detected (PLIP) NAG-NAG.18: 1 residues within 4Å: Chain I: N.1121 No protein-ligand interaction detected (PLIP) NAG-NAG.19: 3 residues within 4Å: Chain I: N.1085, H.1088, F.1090 No protein-ligand interaction detected (PLIP) NAG-NAG.20: 2 residues within 4Å: Chain I: N.704, L.909 1 PLIP interactions: 1 interactions with chain I Hydrophobic interactions: I:L.909 NAG-NAG.21: 3 residues within 4Å: Chain I: N.788, S.790, Q.791 No protein-ligand interaction detected (PLIP)

3 x NAG- NAG- BMA- MAN- MAN: alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-MAN.10: 1 residues within 4Å: Chain G: N.330 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.16: 2 residues within 4Å: Chain H: G.326, N.330 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.22: 3 residues within 4Å: Chain I: G.326, F.329, N.330 No protein-ligand interaction detected (PLIP)

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

NAG.23: 2 residues within 4Å: Chain G: E.268, N.269 Ligand excluded by PLIP NAG.24: 1 residues within 4Å: Chain G: N.644 Ligand excluded by PLIP NAG.25: 2 residues within 4Å: Chain G: N.603, T.605 Ligand excluded by PLIP NAG.26: 2 residues within 4Å: Chain G: N.788, S.790 Ligand excluded by PLIP NAG.27: 1 residues within 4Å: Chain G: N.1061 Ligand excluded by PLIP NAG.28: 1 residues within 4Å: Chain G: N.48 Ligand excluded by PLIP NAG.29: 1 residues within 4Å: Chain G: N.221 Ligand excluded by PLIP NAG.30: 3 residues within 4Å: Chain G: Q.102, N.152, T.154 Ligand excluded by PLIP NAG.31: 1 residues within 4Å: Chain G: N.590 Ligand excluded by PLIP NAG.32: 3 residues within 4Å: Chain G: H.133, N.135, N.136 Ligand excluded by PLIP NAG.33: 2 residues within 4Å: Chain H: N.267, N.269 Ligand excluded by PLIP NAG.34: 1 residues within 4Å: Chain H: N.644 Ligand excluded by PLIP NAG.35: 1 residues within 4Å: Chain H: N.603 Ligand excluded by PLIP NAG.36: 3 residues within 4Å: Chain H: N.696, G.1118 Chain I: D.783 Ligand excluded by PLIP NAG.37: 1 residues within 4Å: Chain H: N.1061 Ligand excluded by PLIP NAG.38: 1 residues within 4Å: Chain H: N.590 Ligand excluded by PLIP NAG.39: 3 residues within 4Å: Chain H: C.2, N.4, N.124 Ligand excluded by PLIP NAG.40: 3 residues within 4Å: Chain H: K.545 Chain I: E.268, N.269 Ligand excluded by PLIP NAG.41: 1 residues within 4Å: Chain I: N.644 Ligand excluded by PLIP NAG.42: 2 residues within 4Å: Chain I: N.603, T.605 Ligand excluded by PLIP NAG.43: 3 residues within 4Å: Chain G: D.783 Chain I: N.696, G.1118 Ligand excluded by PLIP NAG.44: 1 residues within 4Å: Chain I: N.1061 Ligand excluded by PLIP NAG.45: 3 residues within 4Å: Chain I: Y.15, F.46, N.48 Ligand excluded by PLIP NAG.46: 1 residues within 4Å: Chain I: N.221 Ligand excluded by PLIP NAG.47: 2 residues within 4Å: Chain I: N.590, T.591 Ligand excluded by PLIP NAG.48: 1 residues within 4Å: Chain I: N.152 Ligand excluded by PLIP NAG.49: 1 residues within 4Å: Chain I: N.4 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, L. et al., Ultrapotent antibodies against diverse and highly transmissible SARS-CoV-2 variants. Science (2021)

Release Date

2021-07-14

Peptides

antibody A23-58.1 heavy chain: ACE
antibody A23-58.1 light chain: BDF
SARS-CoV-2 spike glycoprotein: GHI

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
F

C
H

E
D

B
G

D
L

F
E

G
A

H
B

I
C

antibody A23-58.1 heavy chain

antibody A23-58.1 light chain

SARS-CoV-2 spike glycoprotein

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