SMTL ID : 7l56.1

Cryo-EM structure of the SARS-CoV-2 spike glycoprotein bound to Fab 2-43

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-mer

Ligands

6 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.1098, T.1100, H.1101 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 3 residues within 4Å: Chain A: N.717, Q.926, Q.1071 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 3 residues within 4Å: Chain B: N.717, Q.926, Q.1071 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 2 residues within 4Å: Chain B: N.1098, T.1100 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 3 residues within 4Å: Chain C: N.717, Q.926, Q.1071 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 7 residues within 4Å: Chain C: S.1097, N.1098, G.1099, T.1100, H.1101, W.1102, F.1103 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- BMA- MAN- NAG- GAL- MAN- MAN: beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[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-NAG-GAL-MAN-MAN.3: 16 residues within 4Å: Chain A: F.338, G.339, N.343, L.368 Chain B: F.486, N.487, Y.489 Chain G: G.103, C.104, S.105, Y.110, L.111, D.112, Y.113, Y.114 Chain H: Y.34 7 PLIP interactions: 4 interactions with chain G, 1 interactions with chain H, 2 interactions with chain B Hydrogen bonds: G:D.112, H:Y.34, G:L.111, G:L.111, G:Y.114, G:Y.114, B:N.487, B:Y.489

1 x NAG- NAG- BMA- MAN- NAG- GAL- MAN- MAN: beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)-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-NAG-GAL-MAN-MAN.4: 12 residues within 4Å: Chain B: G.339, N.343 Chain C: F.486, N.487, Y.489 Chain D: S.105, Y.110, L.111, D.112, Y.113, Y.114 Chain E: D.52 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:Y.113, D:D.112, D:Y.114, C:N.487

1 x NAG- NAG- BMA- MAN- NAG- GAL- MAN- MAN: beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-6)-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-GAL-MAN-MAN.7: 11 residues within 4Å: Chain A: F.486, Y.489 Chain C: G.339, N.343 Chain F: S.105, Y.110, L.111, D.112, Y.113, Y.114 Chain I: Y.34 3 PLIP interactions: 1 interactions with chain F, 1 interactions with chain A, 1 interactions with chain I Hydrogen bonds: F:S.105, F:L.111, F:L.111, F:Y.114, A:Y.489, I:Y.34, F:Y.113

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

NAG.10: 2 residues within 4Å: Chain A: I.1132, N.1134 Ligand excluded by PLIP NAG.11: 2 residues within 4Å: Chain A: E.1072, N.1074 Ligand excluded by PLIP NAG.12: 3 residues within 4Å: Chain A: N.801, S.803, Q.804 Ligand excluded by PLIP NAG.13: 3 residues within 4Å: Chain A: N.709, G.1131 Chain C: D.796 Ligand excluded by PLIP NAG.14: 2 residues within 4Å: Chain A: H.655, N.657 Ligand excluded by PLIP NAG.15: 1 residues within 4Å: Chain A: N.616 Ligand excluded by PLIP NAG.16: 1 residues within 4Å: Chain A: N.603 Ligand excluded by PLIP NAG.17: 2 residues within 4Å: Chain A: F.59, N.61 Ligand excluded by PLIP NAG.18: 1 residues within 4Å: Chain A: N.282 Ligand excluded by PLIP NAG.19: 1 residues within 4Å: Chain A: N.331 Ligand excluded by PLIP NAG.20: 2 residues within 4Å: Chain B: F.59, N.61 Ligand excluded by PLIP NAG.21: 1 residues within 4Å: Chain B: N.282 Ligand excluded by PLIP NAG.22: 2 residues within 4Å: Chain B: N.331, Q.580 Ligand excluded by PLIP NAG.23: 1 residues within 4Å: Chain B: N.603 Ligand excluded by PLIP NAG.24: 2 residues within 4Å: Chain B: H.655, N.657 Ligand excluded by PLIP NAG.25: 1 residues within 4Å: Chain B: N.709 Ligand excluded by PLIP NAG.26: 2 residues within 4Å: Chain B: N.801, Q.804 Ligand excluded by PLIP NAG.27: 2 residues within 4Å: Chain B: E.1072, N.1074 Ligand excluded by PLIP NAG.28: 2 residues within 4Å: Chain B: I.1132, N.1134 Ligand excluded by PLIP NAG.29: 2 residues within 4Å: Chain B: N.164, N.165 Ligand excluded by PLIP NAG.30: 2 residues within 4Å: Chain C: N.164, N.165 Ligand excluded by PLIP NAG.31: 1 residues within 4Å: Chain C: N.282 Ligand excluded by PLIP NAG.32: 2 residues within 4Å: Chain C: N.331, Q.580 Ligand excluded by PLIP NAG.33: 1 residues within 4Å: Chain C: N.603 Ligand excluded by PLIP NAG.34: 2 residues within 4Å: Chain C: N.616, Q.644 Ligand excluded by PLIP NAG.35: 2 residues within 4Å: Chain C: H.655, N.657 Ligand excluded by PLIP NAG.36: 2 residues within 4Å: Chain C: N.709, G.1131 Ligand excluded by PLIP NAG.37: 3 residues within 4Å: Chain C: N.801, S.803, Q.804 Ligand excluded by PLIP NAG.38: 3 residues within 4Å: Chain C: A.706, E.1072, N.1074 Ligand excluded by PLIP NAG.39: 2 residues within 4Å: Chain C: I.1132, N.1134 Ligand excluded by PLIP NAG.40: 2 residues within 4Å: Chain C: Y.28, 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 2-43 variable domain heavy chain: DFG
Fab 2-43 variable domain light chain: EHI

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
F

F
H

G
J

E
G

H
K

I
L

Spike glycoprotein

Fab 2-43 variable domain heavy chain

Fab 2-43 variable domain light chain

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