SMTL ID : 7s0c.1

Structure of the SARS-CoV-2 S 6P trimer in complex with neutralizing antibody N-612-017

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-2-2-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: 3 residues within 4Å: Chain A: N.331, Q.580, L.582 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 4 residues within 4Å: Chain A: N.714, L.919, Q.923, Q.1068 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 4 residues within 4Å: Chain B: N.714, L.919, Q.923, Q.1068 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 2 residues within 4Å: Chain B: N.798, S.800 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 4 residues within 4Å: Chain C: N.1095, T.1097, H.1098, F.1100 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 3 residues within 4Å: Chain C: N.714, L.919, Q.923 No protein-ligand interaction detected (PLIP)

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

NAG.7: 4 residues within 4Å: Chain A: F.338, G.339, F.342, N.343 Ligand excluded by PLIP NAG.8: 2 residues within 4Å: Chain A: Y.28, N.61 Ligand excluded by PLIP NAG.9: 3 residues within 4Å: Chain A: T.108, N.234, T.236 Ligand excluded by PLIP NAG.10: 1 residues within 4Å: Chain A: N.282 Ligand excluded by PLIP NAG.11: 1 residues within 4Å: Chain A: N.616 Ligand excluded by PLIP NAG.12: 3 residues within 4Å: Chain A: N.706, I.1127, G.1128 Ligand excluded by PLIP NAG.13: 3 residues within 4Å: Chain A: N.798, S.800, Q.801 Ligand excluded by PLIP NAG.14: 1 residues within 4Å: Chain A: N.1131 Ligand excluded by PLIP NAG.15: 4 residues within 4Å: Chain A: N.1095, T.1097, H.1098, F.1100 Ligand excluded by PLIP NAG.16: 3 residues within 4Å: Chain A: A.703, E.1069, N.1071 Ligand excluded by PLIP NAG.17: 4 residues within 4Å: Chain B: F.338, F.342, N.343, L.368 Ligand excluded by PLIP NAG.18: 2 residues within 4Å: Chain B: N.331, Q.580 Ligand excluded by PLIP NAG.19: 3 residues within 4Å: Chain A: D.793 Chain B: N.706, G.1128 Ligand excluded by PLIP NAG.20: 1 residues within 4Å: Chain B: N.1131 Ligand excluded by PLIP NAG.21: 4 residues within 4Å: Chain B: N.1095, T.1097, H.1098, F.1100 Ligand excluded by PLIP NAG.22: 3 residues within 4Å: Chain C: N.331, Q.580, L.582 Ligand excluded by PLIP NAG.23: 2 residues within 4Å: Chain C: N.706, N.707 Ligand excluded by PLIP NAG.24: 1 residues within 4Å: Chain C: N.1131 Ligand excluded by PLIP NAG.25: 3 residues within 4Å: Chain C: N.798, S.800, Q.801 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tanaka, S. et al., Rapid identification of neutralizing antibodies against SARS-CoV-2 variants by mRNA display. Cell Rep (2022)

Release Date

2021-10-06

Peptides

Spike glycoprotein: ABC
N-612-017 Fab Heavy Chain: DF
N-612-017 Light Chain: EG

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
A

C
C

D
H

F
M

E
L

G
N

Spike glycoprotein

N-612-017 Fab Heavy Chain

N-612-017 Light Chain

Related Entries With Identical Sequence