SMTL ID : 7l2e.1

Cryo-EM structure of NTD-directed neutralizing antibody 4-18 in complex with prefusion SARS-CoV-2 spike glycoprotein

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-mer

Ligands

24 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.717, L.922, Q.926, Q.1071 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:Q.926 NAG-NAG.2: 3 residues within 4Å: Chain A: N.801, S.803, Q.804 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 4 residues within 4Å: Chain A: N.1098, G.1099, H.1101, F.1103 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:F.1103 NAG-NAG.4: 2 residues within 4Å: Chain A: I.1132, N.1134 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 4 residues within 4Å: Chain A: N.122, T.124, N.125, V.127 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 9 residues within 4Å: Chain A: T.108, N.234, T.236 Chain C: R.457, K.458, S.459, N.460, K.462, E.465 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 4 residues within 4Å: Chain A: N.17 Chain D: N.57, K.58 Chain E: Y.96 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 3 residues within 4Å: Chain A: N.165 Chain C: Y.351, I.468 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 4 residues within 4Å: Chain B: N.717, L.922, Q.926, Q.1071 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:Q.926 NAG-NAG.10: 3 residues within 4Å: Chain B: N.801, S.803, Q.804 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 4 residues within 4Å: Chain B: N.1098, G.1099, H.1101, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 2 residues within 4Å: Chain B: I.1132, N.1134 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 4 residues within 4Å: Chain B: N.122, T.124, N.125, V.127 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 9 residues within 4Å: Chain A: R.457, K.458, S.459, N.460, K.462, E.465 Chain B: T.108, N.234, T.236 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 5 residues within 4Å: Chain B: C.15, N.17 Chain F: N.57, K.58 Chain G: Y.96 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 3 residues within 4Å: Chain A: Y.351, I.468 Chain B: N.165 No protein-ligand interaction detected (PLIP) NAG-NAG.17: 4 residues within 4Å: Chain C: N.717, L.922, Q.926, Q.1071 No protein-ligand interaction detected (PLIP) NAG-NAG.18: 3 residues within 4Å: Chain C: N.801, S.803, Q.804 No protein-ligand interaction detected (PLIP) NAG-NAG.19: 4 residues within 4Å: Chain C: N.1098, G.1099, H.1101, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG.20: 2 residues within 4Å: Chain C: I.1132, N.1134 No protein-ligand interaction detected (PLIP) NAG-NAG.21: 4 residues within 4Å: Chain C: N.122, T.124, N.125, V.127 No protein-ligand interaction detected (PLIP) NAG-NAG.22: 9 residues within 4Å: Chain B: R.457, K.458, S.459, N.460, K.462, E.465 Chain C: T.108, N.234, T.236 No protein-ligand interaction detected (PLIP) NAG-NAG.23: 5 residues within 4Å: Chain C: C.15, N.17 Chain H: N.57, K.58 Chain I: Y.96 No protein-ligand interaction detected (PLIP) NAG-NAG.24: 3 residues within 4Å: Chain B: Y.351, I.468 Chain C: N.165 No protein-ligand interaction detected (PLIP)

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

NAG.25: 4 residues within 4Å: Chain A: A.706, E.1072, K.1073, N.1074 Ligand excluded by PLIP NAG.26: 3 residues within 4Å: Chain A: F.59, N.61, P.631 Ligand excluded by PLIP NAG.27: 3 residues within 4Å: Chain A: N.280, E.281, N.282 Ligand excluded by PLIP NAG.28: 3 residues within 4Å: Chain A: N.149, S.151, W.152 Ligand excluded by PLIP NAG.29: 2 residues within 4Å: Chain A: N.331, Q.580 Ligand excluded by PLIP NAG.30: 3 residues within 4Å: Chain A: N.709, G.1131 Chain B: D.796 Ligand excluded by PLIP NAG.31: 1 residues within 4Å: Chain A: N.657 Ligand excluded by PLIP NAG.32: 2 residues within 4Å: Chain A: N.343, S.371 Ligand excluded by PLIP NAG.33: 1 residues within 4Å: Chain A: N.616 Ligand excluded by PLIP NAG.34: 1 residues within 4Å: Chain A: N.603 Ligand excluded by PLIP NAG.35: 4 residues within 4Å: Chain B: A.706, E.1072, K.1073, N.1074 Ligand excluded by PLIP NAG.36: 3 residues within 4Å: Chain B: F.59, N.61, P.631 Ligand excluded by PLIP NAG.37: 3 residues within 4Å: Chain B: N.280, E.281, N.282 Ligand excluded by PLIP NAG.38: 3 residues within 4Å: Chain B: N.149, S.151, W.152 Ligand excluded by PLIP NAG.39: 2 residues within 4Å: Chain B: N.331, Q.580 Ligand excluded by PLIP NAG.40: 4 residues within 4Å: Chain B: N.709, G.1131 Chain C: K.795, D.796 Ligand excluded by PLIP NAG.41: 1 residues within 4Å: Chain B: N.657 Ligand excluded by PLIP NAG.42: 2 residues within 4Å: Chain B: N.343, S.371 Ligand excluded by PLIP NAG.43: 1 residues within 4Å: Chain B: N.616 Ligand excluded by PLIP NAG.44: 1 residues within 4Å: Chain B: N.603 Ligand excluded by PLIP NAG.45: 4 residues within 4Å: Chain C: A.706, E.1072, K.1073, N.1074 Ligand excluded by PLIP NAG.46: 3 residues within 4Å: Chain C: F.59, N.61, P.631 Ligand excluded by PLIP NAG.47: 3 residues within 4Å: Chain C: N.280, E.281, N.282 Ligand excluded by PLIP NAG.48: 3 residues within 4Å: Chain C: N.149, S.151, W.152 Ligand excluded by PLIP NAG.49: 2 residues within 4Å: Chain C: N.331, Q.580 Ligand excluded by PLIP NAG.50: 3 residues within 4Å: Chain A: D.796 Chain C: N.709, G.1131 Ligand excluded by PLIP NAG.51: 1 residues within 4Å: Chain C: N.657 Ligand excluded by PLIP NAG.52: 2 residues within 4Å: Chain C: N.343, S.371 Ligand excluded by PLIP NAG.53: 2 residues within 4Å: Chain C: N.616, T.618 Ligand excluded by PLIP NAG.54: 1 residues within 4Å: Chain C: N.603 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cerutti, G. et al., Potent SARS-CoV-2 neutralizing antibodies directed against spike N-terminal domain target a single supersite. Cell Host Microbe (2021)

Release Date

2021-03-24

Peptides

Spike glycoprotein: ABC
4-18 heavy chain: DFH
4-18 light chain: EGI

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
H

F
G

H
I

E
L

G
J

I
K

Spike glycoprotein

4-18 heavy chain

4-18 light chain

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