SMTL ID : 7k4n.1

SARS-CoV-2 spike in complex with the S2E12 neutralizing antibody Fab fragment

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-mer

Ligands

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.1: 5 residues within 4Å: Chain A: N.717, L.922, N.925, Q.926, Q.1071 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.922, A:N.925 NAG-NAG.2: 2 residues within 4Å: Chain A: N.1098, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 2 residues within 4Å: Chain A: I.1132, N.1134 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 4 residues within 4Å: Chain A: F.338, G.339, F.342, N.343 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 2 residues within 4Å: Chain A: N.801, S.803 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 5 residues within 4Å: Chain D: N.717, L.922, N.925, Q.926, Q.1071 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:L.922, D:N.925 NAG-NAG.7: 2 residues within 4Å: Chain D: N.1098, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 2 residues within 4Å: Chain D: I.1132, N.1134 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 4 residues within 4Å: Chain D: F.338, G.339, F.342, N.343 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 2 residues within 4Å: Chain D: N.801, S.803 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 5 residues within 4Å: Chain G: N.717, L.922, N.925, Q.926, Q.1071 2 PLIP interactions: 2 interactions with chain G Hydrophobic interactions: G:L.922, G:N.925 NAG-NAG.12: 2 residues within 4Å: Chain G: N.1098, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 2 residues within 4Å: Chain G: I.1132, N.1134 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 4 residues within 4Å: Chain G: F.338, G.339, F.342, N.343 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 2 residues within 4Å: Chain G: N.801, S.803 No protein-ligand interaction detected (PLIP)

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

NAG.16: 3 residues within 4Å: Chain A: N.280, E.281, N.282 Ligand excluded by PLIP NAG.17: 2 residues within 4Å: Chain A: N.603, T.604 Ligand excluded by PLIP NAG.18: 3 residues within 4Å: Chain A: H.655, V.656, N.657 Ligand excluded by PLIP NAG.19: 4 residues within 4Å: Chain A: A.706, E.1072, K.1073, N.1074 Ligand excluded by PLIP NAG.20: 4 residues within 4Å: Chain A: Y.28, T.29, N.30, N.61 Ligand excluded by PLIP NAG.21: 2 residues within 4Å: Chain A: N.616, Q.644 Ligand excluded by PLIP NAG.22: 4 residues within 4Å: Chain A: N.122, A.123, T.124, N.125 Ligand excluded by PLIP NAG.23: 3 residues within 4Å: Chain A: E.132, N.165, T.167 Ligand excluded by PLIP NAG.24: 3 residues within 4Å: Chain A: G.232, I.233, N.234 Ligand excluded by PLIP NAG.25: 3 residues within 4Å: Chain A: N.331, P.579, Q.580 Ligand excluded by PLIP NAG.26: 2 residues within 4Å: Chain A: N.709, G.1131 Ligand excluded by PLIP NAG.27: 3 residues within 4Å: Chain D: N.280, E.281, N.282 Ligand excluded by PLIP NAG.28: 2 residues within 4Å: Chain D: N.603, T.604 Ligand excluded by PLIP NAG.29: 3 residues within 4Å: Chain D: H.655, V.656, N.657 Ligand excluded by PLIP NAG.30: 4 residues within 4Å: Chain D: A.706, E.1072, K.1073, N.1074 Ligand excluded by PLIP NAG.31: 4 residues within 4Å: Chain D: Y.28, T.29, N.30, N.61 Ligand excluded by PLIP NAG.32: 2 residues within 4Å: Chain D: N.616, Q.644 Ligand excluded by PLIP NAG.33: 4 residues within 4Å: Chain D: N.122, A.123, T.124, N.125 Ligand excluded by PLIP NAG.34: 2 residues within 4Å: Chain D: E.132, N.165 Ligand excluded by PLIP NAG.35: 3 residues within 4Å: Chain D: G.232, I.233, N.234 Ligand excluded by PLIP NAG.36: 3 residues within 4Å: Chain D: N.331, P.579, Q.580 Ligand excluded by PLIP NAG.37: 2 residues within 4Å: Chain D: N.709, G.1131 Ligand excluded by PLIP NAG.38: 3 residues within 4Å: Chain G: N.280, E.281, N.282 Ligand excluded by PLIP NAG.39: 2 residues within 4Å: Chain G: N.603, T.604 Ligand excluded by PLIP NAG.40: 3 residues within 4Å: Chain G: H.655, V.656, N.657 Ligand excluded by PLIP NAG.41: 4 residues within 4Å: Chain G: A.706, E.1072, K.1073, N.1074 Ligand excluded by PLIP NAG.42: 4 residues within 4Å: Chain G: Y.28, T.29, N.30, N.61 Ligand excluded by PLIP NAG.43: 2 residues within 4Å: Chain G: N.616, Q.644 Ligand excluded by PLIP NAG.44: 4 residues within 4Å: Chain G: N.122, A.123, T.124, N.125 Ligand excluded by PLIP NAG.45: 3 residues within 4Å: Chain G: E.132, N.165, T.167 Ligand excluded by PLIP NAG.46: 3 residues within 4Å: Chain G: G.232, I.233, N.234 Ligand excluded by PLIP NAG.47: 3 residues within 4Å: Chain G: N.331, P.579, Q.580 Ligand excluded by PLIP NAG.48: 2 residues within 4Å: Chain G: N.709, G.1131 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
S2E12 neutralizing antibody Fab fragment (heavy chain): BEH
S2E12 neutralizing antibody 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

S2E12 neutralizing antibody Fab fragment (heavy chain)

S2E12 neutralizing antibody Fab fragment (light chain)

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