SMTL ID : 7jvc.1

SARS-CoV-2 spike in complex with the S2A4 neutralizing antibody Fab fragment

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-mer

Ligands

12 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.736, T.738, L.941, N.944, Q.945 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.941, A:N.944 NAG-NAG.2: 3 residues within 4Å: Chain A: N.820, S.822, Q.823 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 4 residues within 4Å: Chain A: N.1117, T.1119, H.1120, F.1122 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 1 residues within 4Å: Chain A: N.1153 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 5 residues within 4Å: Chain D: N.736, T.738, L.941, N.944, Q.945 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:L.941, D:N.944 NAG-NAG.7: 3 residues within 4Å: Chain D: N.820, S.822, Q.823 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 4 residues within 4Å: Chain D: N.1117, T.1119, H.1120, F.1122 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 1 residues within 4Å: Chain D: N.1153 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 5 residues within 4Å: Chain G: N.736, T.738, L.941, N.944, Q.945 2 PLIP interactions: 2 interactions with chain G Hydrophobic interactions: G:L.941, G:N.944 NAG-NAG.12: 3 residues within 4Å: Chain G: N.820, S.822, Q.823 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 4 residues within 4Å: Chain G: N.1117, T.1119, H.1120, F.1122 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 1 residues within 4Å: Chain G: N.1153 No protein-ligand interaction detected (PLIP)

3 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.3: 5 residues within 4Å: Chain A: G.358, N.362, V.386, L.387 Chain B: S.56 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.56 NAG-NAG-BMA.8: 5 residues within 4Å: Chain D: G.358, N.362, V.386, L.387 Chain E: S.56 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:S.56 NAG-NAG-BMA.13: 5 residues within 4Å: Chain G: G.358, N.362, V.386, L.387 Chain H: S.56 1 PLIP interactions: 1 interactions with chain H Hydrogen bonds: H:S.56

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

NAG.16: 3 residues within 4Å: Chain A: F.78, S.79, N.80 Ligand excluded by PLIP NAG.17: 4 residues within 4Å: Chain A: N.141, A.142, T.143, N.144 Ligand excluded by PLIP NAG.18: 2 residues within 4Å: Chain A: N.215, N.253 Ligand excluded by PLIP NAG.19: 2 residues within 4Å: Chain A: N.299, N.301 Ligand excluded by PLIP NAG.20: 2 residues within 4Å: Chain A: N.350, Q.599 Ligand excluded by PLIP NAG.21: 2 residues within 4Å: Chain A: N.622, T.623 Ligand excluded by PLIP NAG.22: 3 residues within 4Å: Chain A: N.635, T.637, Q.663 Ligand excluded by PLIP NAG.23: 3 residues within 4Å: Chain A: H.674, V.675, N.676 Ligand excluded by PLIP NAG.24: 2 residues within 4Å: Chain A: N.728, G.1150 Ligand excluded by PLIP NAG.25: 4 residues within 4Å: Chain A: A.725, E.1091, K.1092, N.1093 Ligand excluded by PLIP NAG.26: 2 residues within 4Å: Chain A: E.151, N.184 Ligand excluded by PLIP NAG.27: 3 residues within 4Å: Chain D: F.78, S.79, N.80 Ligand excluded by PLIP NAG.28: 4 residues within 4Å: Chain D: N.141, A.142, T.143, N.144 Ligand excluded by PLIP NAG.29: 2 residues within 4Å: Chain D: N.215, N.253 Ligand excluded by PLIP NAG.30: 2 residues within 4Å: Chain D: N.299, N.301 Ligand excluded by PLIP NAG.31: 2 residues within 4Å: Chain D: N.350, Q.599 Ligand excluded by PLIP NAG.32: 2 residues within 4Å: Chain D: N.622, T.623 Ligand excluded by PLIP NAG.33: 3 residues within 4Å: Chain D: N.635, T.637, Q.663 Ligand excluded by PLIP NAG.34: 3 residues within 4Å: Chain D: H.674, V.675, N.676 Ligand excluded by PLIP NAG.35: 2 residues within 4Å: Chain D: N.728, G.1150 Ligand excluded by PLIP NAG.36: 4 residues within 4Å: Chain D: A.725, E.1091, K.1092, N.1093 Ligand excluded by PLIP NAG.37: 2 residues within 4Å: Chain D: E.151, N.184 Ligand excluded by PLIP NAG.38: 3 residues within 4Å: Chain G: F.78, S.79, N.80 Ligand excluded by PLIP NAG.39: 4 residues within 4Å: Chain G: N.141, A.142, T.143, N.144 Ligand excluded by PLIP NAG.40: 2 residues within 4Å: Chain G: N.215, N.253 Ligand excluded by PLIP NAG.41: 2 residues within 4Å: Chain G: N.299, N.301 Ligand excluded by PLIP NAG.42: 2 residues within 4Å: Chain G: N.350, Q.599 Ligand excluded by PLIP NAG.43: 2 residues within 4Å: Chain G: N.622, T.623 Ligand excluded by PLIP NAG.44: 3 residues within 4Å: Chain G: N.635, T.637, Q.663 Ligand excluded by PLIP NAG.45: 3 residues within 4Å: Chain G: H.674, V.675, N.676 Ligand excluded by PLIP NAG.46: 2 residues within 4Å: Chain G: N.728, G.1150 Ligand excluded by PLIP NAG.47: 4 residues within 4Å: Chain G: A.725, E.1091, K.1092, N.1093 Ligand excluded by PLIP NAG.48: 2 residues within 4Å: Chain G: E.151, N.184 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Piccoli, L. et al., Mapping Neutralizing and Immunodominant Sites on the SARS-CoV-2 Spike Receptor-Binding Domain by Structure-Guided High-Resolution Serology. Cell (2020)

Release Date

2020-10-14

Peptides

Spike glycoprotein: ADG
S2A4 Fab heavy chain: BEH
S2A4 Fab 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

S2A4 Fab heavy chain

S2A4 Fab light chain

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