SMTL ID : 7wpf.1

SARS-CoV-2 Omicron Variant S Trimer complexed with three JMB2002 Fab

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-3-mer

Ligands

2 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: 4 residues within 4Å: Chain A: N.714, L.919, Q.923, Q.1068 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:Q.923 NAG-NAG.2: 5 residues within 4Å: Chain B: N.714, L.919, N.922, Q.923, Q.1068 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:Q.923

35 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)(Non-covalent)

NAG.3: 3 residues within 4Å: Chain A: E.1069, K.1070, N.1071 Ligand excluded by PLIP NAG.4: 3 residues within 4Å: Chain A: T.106, N.231, T.233 Ligand excluded by PLIP NAG.5: 1 residues within 4Å: Chain A: N.279 Ligand excluded by PLIP NAG.6: 3 residues within 4Å: Chain A: N.1095, G.1096, F.1100 Ligand excluded by PLIP NAG.7: 3 residues within 4Å: Chain A: N.798, S.800, Q.801 Ligand excluded by PLIP NAG.8: 2 residues within 4Å: Chain A: N.706, G.1128 Ligand excluded by PLIP NAG.9: 3 residues within 4Å: Chain A: E.651, Y.652, N.654 Ligand excluded by PLIP NAG.10: 2 residues within 4Å: Chain A: N.613, Q.641 Ligand excluded by PLIP NAG.11: 2 residues within 4Å: Chain A: N.600, T.601 Ligand excluded by PLIP NAG.12: 3 residues within 4Å: Chain A: N.328, Q.577, L.579 Ligand excluded by PLIP NAG.13: 2 residues within 4Å: Chain A: S.110, N.160 Ligand excluded by PLIP NAG.14: 4 residues within 4Å: Chain B: A.703, E.1069, K.1070, N.1071 Ligand excluded by PLIP NAG.15: 3 residues within 4Å: Chain B: T.106, N.231, T.233 Ligand excluded by PLIP NAG.16: 1 residues within 4Å: Chain B: N.279 Ligand excluded by PLIP NAG.17: 2 residues within 4Å: Chain B: I.1129, N.1131 Ligand excluded by PLIP NAG.18: 2 residues within 4Å: Chain B: N.1095, F.1100 Ligand excluded by PLIP NAG.19: 2 residues within 4Å: Chain B: N.798, S.800 Ligand excluded by PLIP NAG.20: 3 residues within 4Å: Chain B: N.706, I.1127 Chain C: Y.793 Ligand excluded by PLIP NAG.21: 2 residues within 4Å: Chain B: Y.652, N.654 Ligand excluded by PLIP NAG.22: 2 residues within 4Å: Chain B: N.613, Q.641 Ligand excluded by PLIP NAG.23: 2 residues within 4Å: Chain B: N.600, T.601 Ligand excluded by PLIP NAG.24: 4 residues within 4Å: Chain B: N.328, P.576, Q.577, L.579 Ligand excluded by PLIP NAG.25: 4 residues within 4Å: Chain B: S.110, E.130, N.160, T.162 Ligand excluded by PLIP NAG.26: 1 residues within 4Å: Chain C: N.654 Ligand excluded by PLIP NAG.27: 2 residues within 4Å: Chain C: N.328, Q.577 Ligand excluded by PLIP NAG.28: 2 residues within 4Å: Chain C: N.231, T.233 Ligand excluded by PLIP NAG.29: 1 residues within 4Å: Chain C: N.600 Ligand excluded by PLIP NAG.30: 3 residues within 4Å: Chain C: A.710, E.1069, N.1071 Ligand excluded by PLIP NAG.31: 3 residues within 4Å: Chain C: I.1129, V.1130, N.1131 Ligand excluded by PLIP NAG.32: 4 residues within 4Å: Chain C: N.1095, T.1097, H.1098, F.1100 Ligand excluded by PLIP NAG.33: 3 residues within 4Å: Chain C: S.110, E.130, N.160 Ligand excluded by PLIP NAG.34: 3 residues within 4Å: Chain C: N.613, C.614, Q.641 Ligand excluded by PLIP NAG.35: 1 residues within 4Å: Chain C: N.706 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: E.278, N.279 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yin, W. et al., Structures of the Omicron spike trimer with ACE2 and an anti-Omicron antibody. Science (2022)

Release Date

2022-03-16

Peptides

Spike glycoprotein: ABC
JMB2002 Fab heavy chain: DGJ
JMB2002 Fab light chain: EHK
Anti-Fab nanobody: FIL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
R

G
U

J
X

E
S

H
V

K
Y

F
T

I
W

L
Z

Spike glycoprotein

JMB2002 Fab heavy chain

JMB2002 Fab light chain

Anti-Fab nanobody

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