SMTL ID : 7rkv.1

Structure of the SARS-CoV-2 S 6P trimer in complex with neutralizing antibody C118 (State 1)

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-mer

Ligands

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

NAG.1: 3 residues within 4Å: Chain A: N.280, E.281, N.282 Ligand excluded by PLIP NAG.2: 2 residues within 4Å: Chain A: N.603, T.604 Ligand excluded by PLIP NAG.3: 3 residues within 4Å: Chain A: H.655, V.656, N.657 Ligand excluded by PLIP NAG.4: 3 residues within 4Å: Chain A: A.703, N.1071 Chain B: Q.892 Ligand excluded by PLIP NAG.5: 1 residues within 4Å: Chain A: N.616 Ligand excluded by PLIP NAG.6: 4 residues within 4Å: Chain A: N.122, A.123, T.124, N.125 Ligand excluded by PLIP NAG.7: 1 residues within 4Å: Chain A: N.165 Ligand excluded by PLIP NAG.8: 1 residues within 4Å: Chain A: N.234 Ligand excluded by PLIP NAG.9: 3 residues within 4Å: Chain A: N.331, P.579, Q.580 Ligand excluded by PLIP NAG.10: 3 residues within 4Å: Chain A: N.706, I.1127, G.1128 Ligand excluded by PLIP NAG.11: 2 residues within 4Å: Chain A: N.798, S.800 Ligand excluded by PLIP NAG.12: 4 residues within 4Å: Chain A: N.1095, T.1097, H.1098, F.1100 Ligand excluded by PLIP NAG.13: 1 residues within 4Å: Chain A: N.1131 Ligand excluded by PLIP NAG.14: 1 residues within 4Å: Chain A: N.714 Ligand excluded by PLIP NAG.15: 3 residues within 4Å: Chain B: N.280, E.281, N.282 Ligand excluded by PLIP NAG.16: 2 residues within 4Å: Chain B: N.603, T.604 Ligand excluded by PLIP NAG.17: 3 residues within 4Å: Chain B: H.655, V.656, N.657 Ligand excluded by PLIP NAG.18: 3 residues within 4Å: Chain B: A.703, N.1071 Chain C: Q.892 Ligand excluded by PLIP NAG.19: 1 residues within 4Å: Chain B: N.616 Ligand excluded by PLIP NAG.20: 4 residues within 4Å: Chain B: N.122, A.123, T.124, N.125 Ligand excluded by PLIP NAG.21: 1 residues within 4Å: Chain B: N.165 Ligand excluded by PLIP NAG.22: 1 residues within 4Å: Chain B: N.234 Ligand excluded by PLIP NAG.23: 3 residues within 4Å: Chain B: N.331, P.579, Q.580 Ligand excluded by PLIP NAG.24: 3 residues within 4Å: Chain B: N.706, I.1127, G.1128 Ligand excluded by PLIP NAG.25: 2 residues within 4Å: Chain B: N.798, S.800 Ligand excluded by PLIP NAG.26: 4 residues within 4Å: Chain B: N.1095, G.1096, T.1097, H.1098 Ligand excluded by PLIP NAG.27: 1 residues within 4Å: Chain B: N.1131 Ligand excluded by PLIP NAG.28: 2 residues within 4Å: Chain B: N.714, L.919 Ligand excluded by PLIP NAG.29: 3 residues within 4Å: Chain C: N.280, E.281, N.282 Ligand excluded by PLIP NAG.30: 3 residues within 4Å: Chain C: H.655, V.656, N.657 Ligand excluded by PLIP NAG.31: 5 residues within 4Å: Chain A: Q.892 Chain C: A.703, E.1069, K.1070, N.1071 Ligand excluded by PLIP NAG.32: 1 residues within 4Å: Chain C: N.616 Ligand excluded by PLIP NAG.33: 1 residues within 4Å: Chain C: N.165 Ligand excluded by PLIP NAG.34: 3 residues within 4Å: Chain C: N.331, P.579, Q.580 Ligand excluded by PLIP NAG.35: 3 residues within 4Å: Chain C: N.706, I.1127, G.1128 Ligand excluded by PLIP NAG.36: 2 residues within 4Å: Chain C: N.798, S.800 Ligand excluded by PLIP NAG.37: 2 residues within 4Å: Chain C: N.1095, G.1096 Ligand excluded by PLIP NAG.38: 1 residues within 4Å: Chain C: N.1131 Ligand excluded by PLIP NAG.39: 1 residues within 4Å: Chain C: N.714 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jette, C.A. et al., Broad cross-reactivity across sarbecoviruses exhibited by a subset of COVID-19 donor-derived neutralizing antibodies. Cell Rep (2021)

Release Date

2021-09-22

Peptides

Spike glycoprotein: ABC
C118 Fab Heavy Chain: DFH
C118 Fab Light Chain: EGI

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

F
E

H
G

E
H

G
F

I
L

Spike glycoprotein

C118 Fab Heavy Chain

C118 Fab Light Chain

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