SMTL ID : 7k43.1

SARS-CoV-2 spike in complex with the S2M11 neutralizing antibody Fab fragment

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-mer

Ligands

18 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: C.34, V.35, N.36, N.156 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.156 NAG-NAG.2: 4 residues within 4Å: Chain A: N.141, N.144, E.173, V.190 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:V.190 NAG-NAG.4: 4 residues within 4Å: Chain A: N.736, L.941, Q.945, Q.1090 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.941 NAG-NAG.5: 3 residues within 4Å: Chain A: N.820, S.822, Q.823 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 4 residues within 4Å: Chain A: N.1117, T.1119, H.1120, F.1122 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 1 residues within 4Å: Chain A: N.1153 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 4 residues within 4Å: Chain D: C.34, V.35, N.36, N.156 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.156 NAG-NAG.9: 4 residues within 4Å: Chain D: N.141, N.144, E.173, V.190 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:V.190 NAG-NAG.11: 4 residues within 4Å: Chain D: N.736, L.941, Q.945, Q.1090 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:L.941 NAG-NAG.12: 3 residues within 4Å: Chain D: N.820, S.822, Q.823 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 4 residues within 4Å: Chain D: N.1117, T.1119, H.1120, F.1122 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 1 residues within 4Å: Chain D: N.1153 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 4 residues within 4Å: Chain G: C.34, V.35, N.36, N.156 1 PLIP interactions: 1 interactions with chain G Hydrogen bonds: G:N.156 NAG-NAG.16: 4 residues within 4Å: Chain G: N.141, N.144, E.173, V.190 1 PLIP interactions: 1 interactions with chain G Hydrophobic interactions: G:V.190 NAG-NAG.18: 4 residues within 4Å: Chain G: N.736, L.941, Q.945, Q.1090 1 PLIP interactions: 1 interactions with chain G Hydrophobic interactions: G:L.941 NAG-NAG.19: 3 residues within 4Å: Chain G: N.820, S.822, Q.823 No protein-ligand interaction detected (PLIP) NAG-NAG.20: 4 residues within 4Å: Chain G: N.1117, T.1119, H.1120, F.1122 No protein-ligand interaction detected (PLIP) NAG-NAG.21: 1 residues within 4Å: Chain G: N.1153 No protein-ligand interaction detected (PLIP)

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

NAG-NAG-BMA-FUC.3: 7 residues within 4Å: Chain A: G.358, N.362, V.386 Chain I: S.30, S.31, S.32, Y.33 3 PLIP interactions: 3 interactions with chain I Hydrogen bonds: I:S.30, I:Y.33, I:Y.33 NAG-NAG-BMA-FUC.10: 7 residues within 4Å: Chain C: S.30, S.31, S.32, Y.33 Chain D: G.358, N.362, V.386 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:S.30, C:Y.33, C:Y.33 NAG-NAG-BMA-FUC.17: 7 residues within 4Å: Chain F: S.30, S.31, S.32, Y.33 Chain G: G.358, N.362, V.386 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:S.30, F:Y.33, F:Y.33

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

NAG.22: 2 residues within 4Å: Chain A: N.183, N.184 Ligand excluded by PLIP NAG.23: 2 residues within 4Å: Chain A: T.127, N.253 Ligand excluded by PLIP NAG.24: 3 residues within 4Å: Chain A: Y.47, T.48, N.80 Ligand excluded by PLIP NAG.25: 3 residues within 4Å: Chain A: N.299, N.301 Chain G: K.577 Ligand excluded by PLIP NAG.26: 2 residues within 4Å: Chain A: N.350, Q.599 Ligand excluded by PLIP NAG.27: 1 residues within 4Å: Chain A: N.622 Ligand excluded by PLIP NAG.28: 2 residues within 4Å: Chain A: N.635, Q.663 Ligand excluded by PLIP NAG.29: 3 residues within 4Å: Chain A: H.674, V.675, N.676 Ligand excluded by PLIP NAG.30: 2 residues within 4Å: Chain A: N.728, G.1150 Ligand excluded by PLIP NAG.31: 4 residues within 4Å: Chain A: A.725, E.1091, K.1092, N.1093 Ligand excluded by PLIP NAG.32: 2 residues within 4Å: Chain D: N.183, N.184 Ligand excluded by PLIP NAG.33: 2 residues within 4Å: Chain D: T.127, N.253 Ligand excluded by PLIP NAG.34: 3 residues within 4Å: Chain D: Y.47, T.48, N.80 Ligand excluded by PLIP NAG.35: 3 residues within 4Å: Chain A: K.577 Chain D: N.299, N.301 Ligand excluded by PLIP NAG.36: 2 residues within 4Å: Chain D: N.350, Q.599 Ligand excluded by PLIP NAG.37: 1 residues within 4Å: Chain D: N.622 Ligand excluded by PLIP NAG.38: 2 residues within 4Å: Chain D: N.635, Q.663 Ligand excluded by PLIP NAG.39: 3 residues within 4Å: Chain D: H.674, V.675, N.676 Ligand excluded by PLIP NAG.40: 2 residues within 4Å: Chain D: N.728, G.1150 Ligand excluded by PLIP NAG.41: 4 residues within 4Å: Chain D: A.725, E.1091, K.1092, N.1093 Ligand excluded by PLIP NAG.42: 2 residues within 4Å: Chain G: N.183, N.184 Ligand excluded by PLIP NAG.43: 2 residues within 4Å: Chain G: T.127, N.253 Ligand excluded by PLIP NAG.44: 3 residues within 4Å: Chain G: Y.47, T.48, N.80 Ligand excluded by PLIP NAG.45: 3 residues within 4Å: Chain D: K.577 Chain G: N.299, N.301 Ligand excluded by PLIP NAG.46: 2 residues within 4Å: Chain G: N.350, Q.599 Ligand excluded by PLIP NAG.47: 1 residues within 4Å: Chain G: N.622 Ligand excluded by PLIP NAG.48: 2 residues within 4Å: Chain G: N.635, Q.663 Ligand excluded by PLIP NAG.49: 3 residues within 4Å: Chain G: H.674, V.675, N.676 Ligand excluded by PLIP NAG.50: 2 residues within 4Å: Chain G: N.728, G.1150 Ligand excluded by PLIP NAG.51: 4 residues within 4Å: Chain G: A.725, E.1091, K.1092, N.1093 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tortorici, M.A. et al., Ultrapotent human antibodies protect against SARS-CoV-2 challenge via multiple mechanisms. Science (2020)

Release Date

2020-10-07

Peptides

Spike glycoprotein: ADG
S2M11 Fab fragment (heavy chain): BEH
S2M11 Fab fragment (light chain): CFI

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

D
B

G
E

B
H

E
C

H
F

C
L

F
D

I
G

Spike glycoprotein

S2M11 Fab fragment (heavy chain)

S2M11 Fab fragment (light chain)

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