SMTL ID : 7uar.1

Structure of the SARS-CoV-2 S 6P trimer in complex with the neutralizing antibody Fab fragment, C1717

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY 3.50 Å

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: 2 residues within 4Å: Chain A: N.331, Q.580 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 3 residues within 4Å: Chain A: N.714, L.919, Q.923 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:Q.923 NAG-NAG.4: 4 residues within 4Å: Chain B: F.338, G.339, F.342, N.343 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 3 residues within 4Å: Chain B: N.603 Chain E: S.57, G.58 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 3 residues within 4Å: Chain B: N.714, L.919, Q.923 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:Q.923 NAG-NAG.7: 2 residues within 4Å: Chain C: N.714, Q.923 No protein-ligand interaction detected (PLIP)

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

NAG-NAG-BMA-FUC.3: 5 residues within 4Å: Chain A: K.558 Chain B: N.280, N.282 Chain E: S.68, G.69 No protein-ligand interaction detected (PLIP)

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

NAG.8: 3 residues within 4Å: Chain A: Y.28, N.61 Chain F: L.55 Ligand excluded by PLIP NAG.9: 3 residues within 4Å: Chain A: N.122, T.124, N.125 Ligand excluded by PLIP NAG.10: 2 residues within 4Å: Chain A: T.108, N.234 Ligand excluded by PLIP NAG.11: 4 residues within 4Å: Chain A: N.282 Chain C: K.558 Chain G: G.30, G.69 Ligand excluded by PLIP NAG.12: 3 residues within 4Å: Chain A: F.338, F.342, N.343 Ligand excluded by PLIP NAG.13: 2 residues within 4Å: Chain A: E.309, N.603 Ligand excluded by PLIP NAG.14: 1 residues within 4Å: Chain A: N.706 Ligand excluded by PLIP NAG.15: 2 residues within 4Å: Chain A: N.798, S.800 Ligand excluded by PLIP NAG.16: 3 residues within 4Å: Chain A: N.1095, T.1097, F.1100 Ligand excluded by PLIP NAG.17: 1 residues within 4Å: Chain A: N.1131 Ligand excluded by PLIP NAG.18: 2 residues within 4Å: Chain B: Y.28, N.61 Ligand excluded by PLIP NAG.19: 3 residues within 4Å: Chain B: N.122, A.123, N.125 Ligand excluded by PLIP NAG.20: 3 residues within 4Å: Chain B: E.132, N.165, T.167 Ligand excluded by PLIP NAG.21: 1 residues within 4Å: Chain B: N.331 Ligand excluded by PLIP NAG.22: 3 residues within 4Å: Chain B: N.706, G.1128 Chain C: D.793 Ligand excluded by PLIP NAG.23: 2 residues within 4Å: Chain B: N.798, S.800 Ligand excluded by PLIP NAG.24: 4 residues within 4Å: Chain B: N.1095, T.1097, H.1098, F.1100 Ligand excluded by PLIP NAG.25: 1 residues within 4Å: Chain B: N.1131 Ligand excluded by PLIP NAG.26: 2 residues within 4Å: Chain C: Y.28, N.61 Ligand excluded by PLIP NAG.27: 2 residues within 4Å: Chain B: K.462 Chain C: N.234 Ligand excluded by PLIP NAG.28: 2 residues within 4Å: Chain C: N.331, Q.580 Ligand excluded by PLIP NAG.29: 1 residues within 4Å: Chain C: N.343 Ligand excluded by PLIP NAG.30: 1 residues within 4Å: Chain C: N.603 Ligand excluded by PLIP NAG.31: 1 residues within 4Å: Chain C: N.706 Ligand excluded by PLIP NAG.32: 1 residues within 4Å: Chain C: N.798 Ligand excluded by PLIP NAG.33: 4 residues within 4Å: Chain C: N.1095, T.1097, H.1098, F.1100 Ligand excluded by PLIP NAG.34: 1 residues within 4Å: Chain C: N.1131 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, Z. et al., Analysis of memory B cells identifies conserved neutralizing epitopes on the N-terminal domain of variant SARS-Cov-2 spike proteins. Immunity (2022)

Release Date

2022-04-27

Peptides

Spike glycoprotein: ABC
C1717 Fab Heavy Chain: DFH
C1717 Fab Light Chain: EGI

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
H

F
D

H
F

E
L

G
E

I
G

Spike glycoprotein

C1717 Fab Heavy Chain

C1717 Fab Light Chain

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