SMTL ID : 7sc1.1

Structure of the SARS-CoV-2 S 6P trimer in complex with the human neutralizing antibody Fab fragment, R40-1G8

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-mer

Ligands

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

NAG.1: 2 residues within 4Å: Chain A: Y.28, N.61 Ligand excluded by PLIP NAG.2: 2 residues within 4Å: Chain A: N.122, L.141 Ligand excluded by PLIP NAG.3: 3 residues within 4Å: Chain A: Q.115, E.132, N.165 Ligand excluded by PLIP NAG.4: 2 residues within 4Å: Chain A: G.232, N.234 Ligand excluded by PLIP NAG.5: 3 residues within 4Å: Chain A: N.280, E.281, N.282 Ligand excluded by PLIP NAG.6: 2 residues within 4Å: Chain A: N.331, Q.580 Ligand excluded by PLIP NAG.7: 1 residues within 4Å: Chain A: N.343 Ligand excluded by PLIP NAG.8: 3 residues within 4Å: Chain A: T.307, E.309, N.603 Ligand excluded by PLIP NAG.9: 2 residues within 4Å: Chain A: N.616, T.618 Ligand excluded by PLIP NAG.10: 2 residues within 4Å: Chain A: H.655, N.657 Ligand excluded by PLIP NAG.11: 2 residues within 4Å: Chain A: N.706, G.1128 Ligand excluded by PLIP NAG.12: 3 residues within 4Å: Chain A: N.714, L.919, Q.1068 Ligand excluded by PLIP NAG.13: 2 residues within 4Å: Chain A: A.703, N.1071 Ligand excluded by PLIP NAG.14: 4 residues within 4Å: Chain A: N.1095, T.1097, H.1098, F.1100 Ligand excluded by PLIP NAG.15: 1 residues within 4Å: Chain A: N.1131 Ligand excluded by PLIP NAG.16: 2 residues within 4Å: Chain D: Y.28, N.61 Ligand excluded by PLIP NAG.17: 2 residues within 4Å: Chain D: N.122, L.141 Ligand excluded by PLIP NAG.18: 3 residues within 4Å: Chain D: Q.115, E.132, N.165 Ligand excluded by PLIP NAG.19: 2 residues within 4Å: Chain D: G.232, N.234 Ligand excluded by PLIP NAG.20: 3 residues within 4Å: Chain D: N.280, E.281, N.282 Ligand excluded by PLIP NAG.21: 2 residues within 4Å: Chain D: N.331, Q.580 Ligand excluded by PLIP NAG.22: 1 residues within 4Å: Chain D: N.343 Ligand excluded by PLIP NAG.23: 3 residues within 4Å: Chain D: T.307, E.309, N.603 Ligand excluded by PLIP NAG.24: 2 residues within 4Å: Chain D: N.616, T.618 Ligand excluded by PLIP NAG.25: 2 residues within 4Å: Chain D: H.655, N.657 Ligand excluded by PLIP NAG.26: 2 residues within 4Å: Chain D: N.706, G.1128 Ligand excluded by PLIP NAG.27: 3 residues within 4Å: Chain D: N.714, L.919, Q.1068 Ligand excluded by PLIP NAG.28: 2 residues within 4Å: Chain D: A.703, N.1071 Ligand excluded by PLIP NAG.29: 4 residues within 4Å: Chain D: N.1095, T.1097, H.1098, F.1100 Ligand excluded by PLIP NAG.30: 1 residues within 4Å: Chain D: N.1131 Ligand excluded by PLIP NAG.31: 2 residues within 4Å: Chain G: Y.28, N.61 Ligand excluded by PLIP NAG.32: 2 residues within 4Å: Chain G: N.122, L.141 Ligand excluded by PLIP NAG.33: 3 residues within 4Å: Chain G: Q.115, E.132, N.165 Ligand excluded by PLIP NAG.34: 2 residues within 4Å: Chain G: G.232, N.234 Ligand excluded by PLIP NAG.35: 2 residues within 4Å: Chain G: N.280, N.282 Ligand excluded by PLIP NAG.36: 2 residues within 4Å: Chain G: N.331, Q.580 Ligand excluded by PLIP NAG.37: 1 residues within 4Å: Chain G: N.343 Ligand excluded by PLIP NAG.38: 3 residues within 4Å: Chain G: T.307, E.309, N.603 Ligand excluded by PLIP NAG.39: 2 residues within 4Å: Chain G: N.616, T.618 Ligand excluded by PLIP NAG.40: 2 residues within 4Å: Chain G: H.655, N.657 Ligand excluded by PLIP NAG.41: 2 residues within 4Å: Chain G: N.706, G.1128 Ligand excluded by PLIP NAG.42: 3 residues within 4Å: Chain G: N.714, L.919, Q.1068 Ligand excluded by PLIP NAG.43: 2 residues within 4Å: Chain G: A.703, N.1071 Ligand excluded by PLIP NAG.44: 4 residues within 4Å: Chain G: N.1095, T.1097, H.1098, F.1100 Ligand excluded by PLIP NAG.45: 1 residues within 4Å: Chain G: N.1131 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Vanshylla, K. et al., Discovery of ultrapotent broadly neutralizing antibodies from SARS-CoV-2 elite neutralizers. Cell Host Microbe (2022)

Release Date

2022-02-02

Peptides

Spike glycoprotein: ADG
R40-1G8 Fab heavy chain: BEH
R40-1G8 Fab light chain: CFI

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

D
B

G
C

B
H

E
M

H
P

C
L

F
N

I
Q

Spike glycoprotein

R40-1G8 Fab heavy chain

R40-1G8 Fab light chain

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