SMTL ID : 7rbv.1

SARS-CoV-2 Spike in complex with PVI.V6-14 Fab

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-2-3-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: 2 residues within 4Å: Chain C: N.135, N.136 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 3 residues within 4Å: Chain C: Y.15, F.46, N.48 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 2 residues within 4Å: Chain C: N.704, L.909 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 1 residues within 4Å: Chain C: N.1061 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 3 residues within 4Å: Chain C: N.1085, T.1087, H.1088 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 3 residues within 4Å: Chain F: K.134, N.135, N.136 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 2 residues within 4Å: Chain F: Y.15, N.48 No protein-ligand interaction detected (PLIP) NAG-NAG.17: 2 residues within 4Å: Chain F: N.704, L.909 No protein-ligand interaction detected (PLIP) NAG-NAG.19: 2 residues within 4Å: Chain C: Q.882 Chain F: N.1061 No protein-ligand interaction detected (PLIP) NAG-NAG.20: 4 residues within 4Å: Chain F: N.1085, T.1087, H.1088, F.1090 No protein-ligand interaction detected (PLIP) NAG-NAG.21: 3 residues within 4Å: Chain G: K.134, N.135, N.136 No protein-ligand interaction detected (PLIP) NAG-NAG.26: 2 residues within 4Å: Chain G: F.46, N.48 No protein-ligand interaction detected (PLIP) NAG-NAG.27: 3 residues within 4Å: Chain G: N.704, Q.913, Q.1058 No protein-ligand interaction detected (PLIP) NAG-NAG.29: 2 residues within 4Å: Chain F: Q.882 Chain G: N.1061 No protein-ligand interaction detected (PLIP) NAG-NAG.30: 4 residues within 4Å: Chain G: N.1085, T.1087, H.1088, F.1090 No protein-ligand interaction detected (PLIP)

3 x NAG- NAG- BMA- MAN- MAN: alpha-D-mannopyranose-(1-4)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-MAN.2: 5 residues within 4Å: Chain C: N.109, T.111, N.112, V.114, V.158 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:V.158 NAG-NAG-BMA-MAN-MAN.12: 4 residues within 4Å: Chain F: N.109, T.111, V.114, V.158 1 PLIP interactions: 1 interactions with chain F Hydrophobic interactions: F:V.158 NAG-NAG-BMA-MAN-MAN.22: 5 residues within 4Å: Chain G: N.109, T.111, N.112, V.114, V.158 1 PLIP interactions: 1 interactions with chain G Hydrophobic interactions: G:V.158

3 x NAG- NAG- BMA- MAN- MAN: alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-MAN.3: 2 residues within 4Å: Chain C: N.4, N.124 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.13: 4 residues within 4Å: Chain F: C.2, V.3, N.4, N.124 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.23: 5 residues within 4Å: Chain G: C.2, V.3, N.4, C.123, N.124 No protein-ligand interaction detected (PLIP)

6 x NAG- NAG- BMA- MAN: alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN.4: 4 residues within 4Å: Chain C: T.95, N.221, T.223 Chain F: K.445 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:K.445, F:K.445 NAG-NAG-BMA-MAN.5: 3 residues within 4Å: Chain C: N.267, E.268, N.269 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.14: 3 residues within 4Å: Chain F: N.221, T.223 Chain G: K.445 1 PLIP interactions: 1 interactions with chain G Hydrogen bonds: G:K.445 NAG-NAG-BMA-MAN.15: 3 residues within 4Å: Chain F: N.267, E.268, N.269 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.24: 5 residues within 4Å: Chain C: K.445 Chain G: T.95, N.221, I.222, T.223 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:K.445 NAG-NAG-BMA-MAN.25: 2 residues within 4Å: Chain G: E.268, N.269 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.8: 2 residues within 4Å: Chain C: N.788, S.790 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.18: 2 residues within 4Å: Chain F: N.788, S.790 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.28: 2 residues within 4Å: Chain G: N.788, S.790 No protein-ligand interaction detected (PLIP)

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

NAG.31: 1 residues within 4Å: Chain C: N.318 Ligand excluded by PLIP NAG.32: 1 residues within 4Å: Chain C: N.330 Ligand excluded by PLIP NAG.33: 2 residues within 4Å: Chain C: N.603, W.620 Ligand excluded by PLIP NAG.34: 1 residues within 4Å: Chain C: N.644 Ligand excluded by PLIP NAG.35: 1 residues within 4Å: Chain C: N.696 Ligand excluded by PLIP NAG.36: 1 residues within 4Å: Chain C: N.1121 Ligand excluded by PLIP NAG.37: 1 residues within 4Å: Chain F: N.318 Ligand excluded by PLIP NAG.38: 2 residues within 4Å: Chain F: G.326, N.330 Ligand excluded by PLIP NAG.39: 2 residues within 4Å: Chain F: N.603, W.620 Ligand excluded by PLIP NAG.40: 1 residues within 4Å: Chain F: N.644 Ligand excluded by PLIP NAG.41: 2 residues within 4Å: Chain F: N.696, I.1117 Ligand excluded by PLIP NAG.42: 1 residues within 4Å: Chain F: N.1121 Ligand excluded by PLIP NAG.43: 1 residues within 4Å: Chain G: N.318 Ligand excluded by PLIP NAG.44: 2 residues within 4Å: Chain G: G.326, N.330 Ligand excluded by PLIP NAG.45: 2 residues within 4Å: Chain G: N.603, W.620 Ligand excluded by PLIP NAG.46: 1 residues within 4Å: Chain G: N.644 Ligand excluded by PLIP NAG.47: 1 residues within 4Å: Chain G: N.696 Ligand excluded by PLIP NAG.48: 1 residues within 4Å: Chain G: N.1121 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Altomare, C.G. et al., Structure of a Vaccine-Induced, Germline-Encoded Human Antibody Defines a Neutralizing Epitope on the SARS-CoV-2 Spike N-Terminal Domain. Mbio (2022)

Release Date

2022-05-04

Peptides

PVI.V6-14 Fab light chain, variable region: AD
PVI.V6-14 Fab heavy chain, variable region: BE
Spike glycoprotein: CFG

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
l

D
L

B
h

E
H

C
A

F
B

G
C

PVI.V6-14 Fab light chain, variable region

PVI.V6-14 Fab heavy chain, variable region

Spike glycoprotein

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