SMTL ID : 7l2f.1

Cryo-EM structure of NTD-directed neutralizing antibody 5-24 in complex with prefusion SARS-CoV-2 spike glycoprotein

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-mer

Ligands

16 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.717, Q.926, Q.1071 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 4 residues within 4Å: Chain A: K.795, N.801, S.803, Q.804 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 4 residues within 4Å: Chain A: N.1098, T.1100, H.1101, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 1 residues within 4Å: Chain A: N.1134 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 6 residues within 4Å: Chain A: N.122, A.123, T.124, N.125, V.127, F.157 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 4 residues within 4Å: Chain B: N.717, L.922, Q.926, Q.1071 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 3 residues within 4Å: Chain B: N.801, S.803, Q.804 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 3 residues within 4Å: Chain B: N.1098, T.1100, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 1 residues within 4Å: Chain B: N.1134 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 6 residues within 4Å: Chain B: N.122, T.124, N.125, V.127, F.157, V.171 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.125 NAG-NAG.12: 6 residues within 4Å: Chain A: R.457, K.458, S.459 Chain B: T.108, N.234, T.236 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 3 residues within 4Å: Chain C: N.717, L.922, Q.926 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 3 residues within 4Å: Chain C: N.801, S.803, Q.804 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 4 residues within 4Å: Chain C: N.1098, T.1100, H.1101, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 1 residues within 4Å: Chain C: N.1134 No protein-ligand interaction detected (PLIP) NAG-NAG.17: 5 residues within 4Å: Chain C: N.122, T.124, N.125, V.127, F.157 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.125

2 x NAG- NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA.6: 6 residues within 4Å: Chain A: T.108, N.234, T.236 Chain C: R.457, K.458, S.459 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.18: 8 residues within 4Å: Chain B: R.457, K.458, S.459, N.460, K.462 Chain C: T.108, N.234, T.236 No protein-ligand interaction detected (PLIP)

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

NAG.19: 4 residues within 4Å: Chain A: N.709, I.1130, G.1131 Chain B: D.796 Ligand excluded by PLIP NAG.20: 3 residues within 4Å: Chain A: E.1072, K.1073, N.1074 Ligand excluded by PLIP NAG.21: 1 residues within 4Å: Chain A: N.657 Ligand excluded by PLIP NAG.22: 2 residues within 4Å: Chain A: N.616, T.618 Ligand excluded by PLIP NAG.23: 2 residues within 4Å: Chain A: N.331, Q.580 Ligand excluded by PLIP NAG.24: 1 residues within 4Å: Chain A: N.603 Ligand excluded by PLIP NAG.25: 3 residues within 4Å: Chain A: E.340, N.343, S.371 Ligand excluded by PLIP NAG.26: 1 residues within 4Å: Chain A: N.61 Ligand excluded by PLIP NAG.27: 3 residues within 4Å: Chain A: N.149, S.151, W.152 Ligand excluded by PLIP NAG.28: 5 residues within 4Å: Chain A: E.132, N.164, N.165 Chain C: Y.351, T.470 Ligand excluded by PLIP NAG.29: 4 residues within 4Å: Chain A: N.280, E.281, N.282 Chain C: K.558 Ligand excluded by PLIP NAG.30: 3 residues within 4Å: Chain A: N.17, N.137 Chain D: T.28 Ligand excluded by PLIP NAG.31: 2 residues within 4Å: Chain B: E.1072, N.1074 Ligand excluded by PLIP NAG.32: 2 residues within 4Å: Chain B: N.616, E.619 Ligand excluded by PLIP NAG.33: 1 residues within 4Å: Chain B: N.657 Ligand excluded by PLIP NAG.34: 1 residues within 4Å: Chain B: N.603 Ligand excluded by PLIP NAG.35: 2 residues within 4Å: Chain B: N.709 Chain C: K.795 Ligand excluded by PLIP NAG.36: 2 residues within 4Å: Chain B: F.59, N.61 Ligand excluded by PLIP NAG.37: 3 residues within 4Å: Chain B: N.149, S.151, W.152 Ligand excluded by PLIP NAG.38: 4 residues within 4Å: Chain A: Y.351 Chain B: E.132, N.164, N.165 Ligand excluded by PLIP NAG.39: 3 residues within 4Å: Chain B: N.331, P.579, Q.580 Ligand excluded by PLIP NAG.40: 4 residues within 4Å: Chain B: N.17 Chain H: Q.1, L.27, T.28 Ligand excluded by PLIP NAG.41: 4 residues within 4Å: Chain A: K.558 Chain B: N.280, E.281, N.282 Ligand excluded by PLIP NAG.42: 3 residues within 4Å: Chain B: G.339, N.343, S.371 Ligand excluded by PLIP NAG.43: 2 residues within 4Å: Chain C: N.709, G.1131 Ligand excluded by PLIP NAG.44: 3 residues within 4Å: Chain C: E.1072, K.1073, N.1074 Ligand excluded by PLIP NAG.45: 3 residues within 4Å: Chain C: N.343, S.371, A.372 Ligand excluded by PLIP NAG.46: 2 residues within 4Å: Chain C: H.655, N.657 Ligand excluded by PLIP NAG.47: 2 residues within 4Å: Chain C: N.616, T.618 Ligand excluded by PLIP NAG.48: 1 residues within 4Å: Chain C: N.603 Ligand excluded by PLIP NAG.49: 3 residues within 4Å: Chain C: N.331, Q.580, T.581 Ligand excluded by PLIP NAG.50: 2 residues within 4Å: Chain C: F.59, N.61 Ligand excluded by PLIP NAG.51: 3 residues within 4Å: Chain C: N.149, S.151, W.152 Ligand excluded by PLIP NAG.52: 3 residues within 4Å: Chain C: E.132, N.164, N.165 Ligand excluded by PLIP NAG.53: 3 residues within 4Å: Chain C: N.280, E.281, N.282 Ligand excluded by PLIP NAG.54: 3 residues within 4Å: Chain C: N.17 Chain F: Q.1, T.28 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
5-24 heavy chain: DFH
5-24 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

5-24 heavy chain

5-24 light chain

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