SMTL ID : 7rw2.1

Cryo-EM structure of NTD-directed neutralizing antibody 5-7 in complex with prefusion SARS-CoV-2 spike glycoprotein

Coordinates

PDB Format

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: 8 residues within 4Å: Chain A: T.108, N.234, T.236 Chain B: R.457, K.458, S.459, N.460, E.465 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 5 residues within 4Å: Chain A: N.122, T.124, N.125, V.127, V.171 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:V.171 NAG-NAG.3: 8 residues within 4Å: Chain B: T.108, N.234, T.236 Chain C: R.457, K.458, S.459, N.460, E.465 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 5 residues within 4Å: Chain B: N.122, T.124, N.125, V.127, V.171 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:V.171 NAG-NAG.5: 8 residues within 4Å: Chain A: R.457, K.458, S.459, N.460, E.465 Chain C: T.108, N.234, T.236 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 5 residues within 4Å: Chain C: N.122, T.124, N.125, V.127, V.171 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:V.171

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

NAG.7: 2 residues within 4Å: Chain A: N.343, S.371 Ligand excluded by PLIP NAG.8: 3 residues within 4Å: Chain A: C.15, N.17, N.137 Ligand excluded by PLIP NAG.9: 2 residues within 4Å: Chain A: Y.28, N.61 Ligand excluded by PLIP NAG.10: 2 residues within 4Å: Chain A: N.165 Chain B: Y.351 Ligand excluded by PLIP NAG.11: 1 residues within 4Å: Chain A: N.282 Ligand excluded by PLIP NAG.12: 2 residues within 4Å: Chain A: N.616, T.618 Ligand excluded by PLIP NAG.13: 3 residues within 4Å: Chain A: N.801, S.803, Q.804 Ligand excluded by PLIP NAG.14: 3 residues within 4Å: Chain A: A.706, N.1074 Chain C: Q.895 Ligand excluded by PLIP NAG.15: 4 residues within 4Å: Chain A: H.146, N.148, N.149, S.151 Ligand excluded by PLIP NAG.16: 1 residues within 4Å: Chain A: N.657 Ligand excluded by PLIP NAG.17: 3 residues within 4Å: Chain A: N.1098, T.1100, H.1101 Ligand excluded by PLIP NAG.18: 2 residues within 4Å: Chain A: N.709 Chain C: D.796 Ligand excluded by PLIP NAG.19: 3 residues within 4Å: Chain A: T.716, N.717, Q.1071 Ligand excluded by PLIP NAG.20: 1 residues within 4Å: Chain A: N.1134 Ligand excluded by PLIP NAG.21: 1 residues within 4Å: Chain A: N.603 Ligand excluded by PLIP NAG.22: 2 residues within 4Å: Chain A: N.331, Q.580 Ligand excluded by PLIP NAG.23: 2 residues within 4Å: Chain B: N.343, S.371 Ligand excluded by PLIP NAG.24: 3 residues within 4Å: Chain B: C.15, N.17, N.137 Ligand excluded by PLIP NAG.25: 2 residues within 4Å: Chain B: Y.28, N.61 Ligand excluded by PLIP NAG.26: 2 residues within 4Å: Chain B: N.165 Chain C: Y.351 Ligand excluded by PLIP NAG.27: 1 residues within 4Å: Chain B: N.282 Ligand excluded by PLIP NAG.28: 2 residues within 4Å: Chain B: N.616, T.618 Ligand excluded by PLIP NAG.29: 3 residues within 4Å: Chain B: N.801, S.803, Q.804 Ligand excluded by PLIP NAG.30: 2 residues within 4Å: Chain A: Q.895 Chain B: N.1074 Ligand excluded by PLIP NAG.31: 4 residues within 4Å: Chain B: H.146, N.148, N.149, S.151 Ligand excluded by PLIP NAG.32: 1 residues within 4Å: Chain B: N.657 Ligand excluded by PLIP NAG.33: 2 residues within 4Å: Chain B: N.1098, H.1101 Ligand excluded by PLIP NAG.34: 2 residues within 4Å: Chain A: D.796 Chain B: N.709 Ligand excluded by PLIP NAG.35: 4 residues within 4Å: Chain B: N.717, L.922, Q.926, Q.1071 Ligand excluded by PLIP NAG.36: 1 residues within 4Å: Chain B: N.1134 Ligand excluded by PLIP NAG.37: 2 residues within 4Å: Chain B: N.603, T.604 Ligand excluded by PLIP NAG.38: 2 residues within 4Å: Chain B: N.331, Q.580 Ligand excluded by PLIP NAG.39: 2 residues within 4Å: Chain C: N.343, S.371 Ligand excluded by PLIP NAG.40: 3 residues within 4Å: Chain C: C.15, N.17, N.137 Ligand excluded by PLIP NAG.41: 2 residues within 4Å: Chain C: Y.28, N.61 Ligand excluded by PLIP NAG.42: 3 residues within 4Å: Chain A: Y.351, I.468 Chain C: N.165 Ligand excluded by PLIP NAG.43: 1 residues within 4Å: Chain C: N.282 Ligand excluded by PLIP NAG.44: 2 residues within 4Å: Chain C: N.616, T.618 Ligand excluded by PLIP NAG.45: 3 residues within 4Å: Chain C: N.801, S.803, Q.804 Ligand excluded by PLIP NAG.46: 2 residues within 4Å: Chain B: Q.895 Chain C: N.1074 Ligand excluded by PLIP NAG.47: 4 residues within 4Å: Chain C: H.146, N.148, N.149, S.151 Ligand excluded by PLIP NAG.48: 1 residues within 4Å: Chain C: N.657 Ligand excluded by PLIP NAG.49: 3 residues within 4Å: Chain C: N.1098, T.1100, H.1101 Ligand excluded by PLIP NAG.50: 1 residues within 4Å: Chain C: N.603 Ligand excluded by PLIP NAG.51: 3 residues within 4Å: Chain C: N.717, L.922, Q.926 Ligand excluded by PLIP NAG.52: 1 residues within 4Å: Chain C: N.1134 Ligand excluded by PLIP NAG.53: 2 residues within 4Å: Chain C: N.331, Q.580 Ligand excluded by PLIP NAG.54: 4 residues within 4Å: Chain B: D.796 Chain C: S.708, N.709, N.710 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cerutti, G. et al., Neutralizing antibody 5-7 defines a distinct site of vulnerability in SARS-CoV-2 spike N-terminal domain. Cell Rep (2021)

Release Date

2021-09-01

Peptides

Spike glycoprotein: ABC
5-7 heavy chain: DFH
5-7 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

5-7 heavy chain

5-7 light chain

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