SMTL ID : 9bj3.1

Structure of the SARS-CoV-2 S 6P trimer complex with the human neutralizing antibody Fab fragment, C1596

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-mer

Ligands

21 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 A: N.122, V.127 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 3 residues within 4Å: Chain A: N.280, E.281, N.282 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 2 residues within 4Å: Chain A: N.331, Q.580 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 4 residues within 4Å: Chain A: F.338, G.339, F.342, N.343 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 2 residues within 4Å: Chain A: N.706, G.1128 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 3 residues within 4Å: Chain A: N.1095, H.1098, F.1100 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 1 residues within 4Å: Chain A: N.1131 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 2 residues within 4Å: Chain B: N.122, V.127 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 3 residues within 4Å: Chain B: N.280, E.281, N.282 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 2 residues within 4Å: Chain B: N.331, Q.580 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 4 residues within 4Å: Chain B: F.338, G.339, F.342, N.343 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 2 residues within 4Å: Chain B: N.706, G.1128 No protein-ligand interaction detected (PLIP) NAG-NAG.19: 3 residues within 4Å: Chain B: N.1095, H.1098, F.1100 No protein-ligand interaction detected (PLIP) NAG-NAG.20: 1 residues within 4Å: Chain B: N.1131 No protein-ligand interaction detected (PLIP) NAG-NAG.21: 2 residues within 4Å: Chain I: N.122, N.125 No protein-ligand interaction detected (PLIP) NAG-NAG.23: 3 residues within 4Å: Chain I: N.280, E.281, N.282 No protein-ligand interaction detected (PLIP) NAG-NAG.24: 2 residues within 4Å: Chain I: N.331, Q.580 No protein-ligand interaction detected (PLIP) NAG-NAG.25: 4 residues within 4Å: Chain I: F.338, G.339, F.342, N.343 No protein-ligand interaction detected (PLIP) NAG-NAG.26: 1 residues within 4Å: Chain I: N.706 No protein-ligand interaction detected (PLIP) NAG-NAG.29: 3 residues within 4Å: Chain I: N.1095, H.1098, F.1100 No protein-ligand interaction detected (PLIP) NAG-NAG.30: 1 residues within 4Å: Chain I: N.1131 No protein-ligand interaction detected (PLIP)

3 x NAG- NAG- BMA- MAN: alpha-D-mannopyranose-(1-3)-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.2: 2 residues within 4Å: Chain A: N.234 Chain D: S.28 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:S.28 NAG-NAG-BMA-MAN.12: 2 residues within 4Å: Chain B: N.234 Chain F: S.28 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:S.28 NAG-NAG-BMA-MAN.22: 2 residues within 4Å: Chain H: S.28 Chain I: N.234 1 PLIP interactions: 1 interactions with chain H Hydrogen bonds: H:S.28

6 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.7: 3 residues within 4Å: Chain A: N.714, L.919, Q.1068 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.919 NAG-NAG-BMA.8: 3 residues within 4Å: Chain A: N.798, S.800, Q.801 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.17: 4 residues within 4Å: Chain B: N.714, L.919, Q.923, Q.1068 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:L.919 NAG-NAG-BMA.18: 3 residues within 4Å: Chain B: N.798, S.800, Q.801 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.27: 3 residues within 4Å: Chain I: N.714, L.919, Q.1068 1 PLIP interactions: 1 interactions with chain I Hydrophobic interactions: I:L.919 NAG-NAG-BMA.28: 3 residues within 4Å: Chain I: N.798, S.800, Q.801 No protein-ligand interaction detected (PLIP)

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

NAG.31: 2 residues within 4Å: Chain A: F.59, N.61 Ligand excluded by PLIP NAG.32: 1 residues within 4Å: Chain A: N.165 Ligand excluded by PLIP NAG.33: 1 residues within 4Å: Chain A: N.603 Ligand excluded by PLIP NAG.34: 2 residues within 4Å: Chain A: N.616, T.618 Ligand excluded by PLIP NAG.35: 2 residues within 4Å: Chain A: H.655, N.657 Ligand excluded by PLIP NAG.36: 2 residues within 4Å: Chain A: A.703, N.1071 Ligand excluded by PLIP NAG.37: 1 residues within 4Å: Chain B: N.61 Ligand excluded by PLIP NAG.38: 1 residues within 4Å: Chain B: N.165 Ligand excluded by PLIP NAG.39: 1 residues within 4Å: Chain B: N.603 Ligand excluded by PLIP NAG.40: 2 residues within 4Å: Chain B: N.616, T.618 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: A.703, N.1071 Ligand excluded by PLIP NAG.43: 2 residues within 4Å: Chain I: F.59, N.61 Ligand excluded by PLIP NAG.44: 1 residues within 4Å: Chain I: N.165 Ligand excluded by PLIP NAG.45: 1 residues within 4Å: Chain I: N.603 Ligand excluded by PLIP NAG.46: 2 residues within 4Å: Chain I: N.616, T.618 Ligand excluded by PLIP NAG.47: 2 residues within 4Å: Chain I: H.655, N.657 Ligand excluded by PLIP NAG.48: 2 residues within 4Å: Chain I: A.703, N.1071 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Rubio, A.A. et al., Bispecific antibodies targeting the N-terminal and receptor binding domains potently neutralize SARS-CoV-2 variants of concern. Sci Transl Med (2025)

Release Date

2025-03-05

Peptides

Spike glycoprotein: ABI
C1596 Fab Heavy Chain: CEG
C1596 Light Chain: DFH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

I
S

C
C

E
E

G
H

D
D

F
F

H
L

Spike glycoprotein

C1596 Fab Heavy Chain

C1596 Light Chain

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