SMTL ID : 7mm0.1

Cryo-EM structure of SARS-CoV-2 spike in complex with neutralizing antibody B1-182.1 that targets the receptor-binding domain

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-3-mer

Ligands

13 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 C: N.318, Q.567 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 2 residues within 4Å: Chain C: I.1119, N.1121 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 4 residues within 4Å: Chain C: N.1085, T.1087, H.1088, F.1090 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 1 residues within 4Å: Chain C: N.704 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 4 residues within 4Å: Chain C: N.696, I.1117, G.1118 Chain D: D.783 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 1 residues within 4Å: Chain D: N.1121 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 3 residues within 4Å: Chain D: N.1085, H.1088, F.1090 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 2 residues within 4Å: Chain D: N.704, Q.1058 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 3 residues within 4Å: Chain D: N.788, S.790, Q.791 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 1 residues within 4Å: Chain E: N.1121 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 4 residues within 4Å: Chain E: N.1085, T.1087, H.1088, F.1090 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 3 residues within 4Å: Chain E: N.704, T.706, L.909 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 3 residues within 4Å: Chain E: N.788, S.790, Q.791 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.10: 2 residues within 4Å: Chain E: N.318, Q.567 No protein-ligand interaction detected (PLIP)

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

NAG.15: 2 residues within 4Å: Chain C: N.267, N.269 Ligand excluded by PLIP NAG.16: 1 residues within 4Å: Chain C: N.644 Ligand excluded by PLIP NAG.17: 1 residues within 4Å: Chain C: N.603 Ligand excluded by PLIP NAG.18: 2 residues within 4Å: Chain C: N.788, S.790 Ligand excluded by PLIP NAG.19: 1 residues within 4Å: Chain C: N.1061 Ligand excluded by PLIP NAG.20: 3 residues within 4Å: Chain C: Y.15, F.46, N.48 Ligand excluded by PLIP NAG.21: 1 residues within 4Å: Chain C: N.221 Ligand excluded by PLIP NAG.22: 4 residues within 4Å: Chain C: E.119, N.151, N.152, T.154 Ligand excluded by PLIP NAG.23: 1 residues within 4Å: Chain C: N.590 Ligand excluded by PLIP NAG.24: 3 residues within 4Å: Chain C: H.133, N.135, N.136 Ligand excluded by PLIP NAG.25: 3 residues within 4Å: Chain C: K.545 Chain D: E.268, N.269 Ligand excluded by PLIP NAG.26: 1 residues within 4Å: Chain D: N.644 Ligand excluded by PLIP NAG.27: 2 residues within 4Å: Chain D: N.603, T.605 Ligand excluded by PLIP NAG.28: 2 residues within 4Å: Chain D: N.696 Chain E: D.783 Ligand excluded by PLIP NAG.29: 2 residues within 4Å: Chain D: A.693, N.1061 Ligand excluded by PLIP NAG.30: 2 residues within 4Å: Chain D: T.294, N.590 Ligand excluded by PLIP NAG.31: 1 residues within 4Å: Chain D: N.318 Ligand excluded by PLIP NAG.32: 2 residues within 4Å: Chain E: E.268, N.269 Ligand excluded by PLIP NAG.33: 1 residues within 4Å: Chain E: N.644 Ligand excluded by PLIP NAG.34: 1 residues within 4Å: Chain E: N.603 Ligand excluded by PLIP NAG.35: 3 residues within 4Å: Chain C: D.783 Chain E: N.696, G.1118 Ligand excluded by PLIP NAG.36: 2 residues within 4Å: Chain E: A.693, N.1061 Ligand excluded by PLIP NAG.37: 2 residues within 4Å: Chain E: Y.15, N.48 Ligand excluded by PLIP NAG.38: 5 residues within 4Å: Chain D: K.449, E.452 Chain E: T.95, T.101, N.221 Ligand excluded by PLIP NAG.39: 3 residues within 4Å: Chain E: T.294, T.589, N.590 Ligand excluded by PLIP NAG.40: 1 residues within 4Å: Chain E: N.152 Ligand excluded by PLIP NAG.41: 5 residues within 4Å: Chain E: Q.1, C.2, V.3, N.4, N.124 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

2021-07-28

Peptides

B1-182.1 Fab heavy chain: A
B1-182.1 Fab light chain: B
Spike glycoprotein: CDE

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
H

B
L

C
A

D
B

E
C

B1-182.1 Fab heavy chain

B1-182.1 Fab light chain

Spike glycoprotein

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