SMTL ID : 7l57.1

Cryo-EM structure of the SARS-CoV-2 spike glycoprotein bound to Fab 2-15

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-1-1-mer

Ligands

7 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: 4 residues within 4Å: Chain A: N.1098, G.1099, T.1100, H.1101 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 1 residues within 4Å: Chain A: N.717 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 1 residues within 4Å: Chain B: N.717 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 2 residues within 4Å: Chain B: N.1098, G.1099 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 3 residues within 4Å: Chain C: G.339, E.340, N.343 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 1 residues within 4Å: Chain C: N.717 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 4 residues within 4Å: Chain C: S.1097, N.1098, T.1100, H.1101 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- BMA- MAN- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-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-NAG.3: 6 residues within 4Å: Chain A: F.338, G.339, F.342, N.343, V.367, S.371 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- BMA- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-NAG.6: 5 residues within 4Å: Chain B: G.339, N.343, S.373 Chain C: G.485, F.486 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:G.485

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

NAG.10: 1 residues within 4Å: Chain A: N.1134 Ligand excluded by PLIP NAG.11: 4 residues within 4Å: Chain A: A.713, E.1072, K.1073, N.1074 Ligand excluded by PLIP NAG.12: 1 residues within 4Å: Chain A: N.801 Ligand excluded by PLIP NAG.13: 1 residues within 4Å: Chain A: N.709 Ligand excluded by PLIP NAG.14: 1 residues within 4Å: Chain A: N.657 Ligand excluded by PLIP NAG.15: 2 residues within 4Å: Chain A: N.616, T.618 Ligand excluded by PLIP NAG.16: 2 residues within 4Å: Chain A: N.603, T.604 Ligand excluded by PLIP NAG.17: 3 residues within 4Å: Chain A: T.29, S.60, N.61 Ligand excluded by PLIP NAG.18: 3 residues within 4Å: Chain A: N.280, E.281, N.282 Ligand excluded by PLIP NAG.19: 2 residues within 4Å: Chain A: N.331, Q.580 Ligand excluded by PLIP NAG.20: 2 residues within 4Å: Chain B: Y.28, N.61 Ligand excluded by PLIP NAG.21: 1 residues within 4Å: Chain B: N.282 Ligand excluded by PLIP NAG.22: 3 residues within 4Å: Chain B: N.331, I.332, T.333 Ligand excluded by PLIP NAG.23: 2 residues within 4Å: Chain B: N.603, T.604 Ligand excluded by PLIP NAG.24: 3 residues within 4Å: Chain B: H.655, V.656, N.657 Ligand excluded by PLIP NAG.25: 2 residues within 4Å: Chain B: N.709, N.710 Ligand excluded by PLIP NAG.26: 1 residues within 4Å: Chain B: N.801 Ligand excluded by PLIP NAG.27: 4 residues within 4Å: Chain B: A.713, E.1072, K.1073, N.1074 Ligand excluded by PLIP NAG.28: 3 residues within 4Å: Chain B: I.1132, V.1133, N.1134 Ligand excluded by PLIP NAG.29: 2 residues within 4Å: Chain B: T.114, N.165 Ligand excluded by PLIP NAG.30: 1 residues within 4Å: Chain C: N.165 Ligand excluded by PLIP NAG.31: 2 residues within 4Å: Chain C: N.280, N.282 Ligand excluded by PLIP NAG.32: 4 residues within 4Å: Chain C: N.331, P.579, Q.580, T.581 Ligand excluded by PLIP NAG.33: 2 residues within 4Å: Chain C: N.603, T.604 Ligand excluded by PLIP NAG.34: 1 residues within 4Å: Chain C: N.616 Ligand excluded by PLIP NAG.35: 3 residues within 4Å: Chain C: H.655, V.656, N.657 Ligand excluded by PLIP NAG.36: 3 residues within 4Å: Chain B: D.796 Chain C: N.709, N.710 Ligand excluded by PLIP NAG.37: 1 residues within 4Å: Chain C: N.801 Ligand excluded by PLIP NAG.38: 2 residues within 4Å: Chain C: K.1073, N.1074 Ligand excluded by PLIP NAG.39: 3 residues within 4Å: Chain C: I.1132, V.1133, N.1134 Ligand excluded by PLIP NAG.40: 5 residues within 4Å: Chain C: Y.28, T.29, N.30, S.60, N.61 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Rapp, M. et al., Modular basis for potent SARS-CoV-2 neutralization by a prevalent VH1-2-derived antibody class. Cell Rep (2021)

Release Date

2021-04-14

Peptides

Spike glycoprotein: ABC
Fab 2-15 variable domain heavy chain: D
Fab 2-15 variable domain light chain: E

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
H

E
L

Spike glycoprotein

Fab 2-15 variable domain heavy chain

Fab 2-15 variable domain light chain

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