SMTL ID : 7wpd.1

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

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-1-1-1-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 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 2 residues within 4Å: Chain C: N.714, Q.1068 No protein-ligand interaction detected (PLIP)

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

NAG.3: 3 residues within 4Å: Chain A: A.703, E.1069, 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: 1 residues within 4Å: Chain A: N.1131 Ligand excluded by PLIP NAG.7: 4 residues within 4Å: Chain A: N.1095, G.1096, H.1098, F.1100 Ligand excluded by PLIP NAG.8: 3 residues within 4Å: Chain A: N.798, S.800, Q.801 Ligand excluded by PLIP NAG.9: 2 residues within 4Å: Chain A: N.706 Chain B: Y.793 Ligand excluded by PLIP NAG.10: 2 residues within 4Å: Chain A: Y.652, N.654 Ligand excluded by PLIP NAG.11: 1 residues within 4Å: Chain A: N.613 Ligand excluded by PLIP NAG.12: 2 residues within 4Å: Chain A: N.600, T.601 Ligand excluded by PLIP NAG.13: 4 residues within 4Å: Chain A: N.328, P.576, Q.577, L.579 Ligand excluded by PLIP NAG.14: 1 residues within 4Å: Chain B: N.600 Ligand excluded by PLIP NAG.15: 2 residues within 4Å: Chain B: N.277, N.279 Ligand excluded by PLIP NAG.16: 1 residues within 4Å: Chain B: N.654 Ligand excluded by PLIP NAG.17: 4 residues within 4Å: Chain B: N.328, P.576, Q.577, L.579 Ligand excluded by PLIP NAG.18: 1 residues within 4Å: Chain B: N.1131 Ligand excluded by PLIP NAG.19: 2 residues within 4Å: Chain B: N.231, T.233 Ligand excluded by PLIP NAG.20: 5 residues within 4Å: Chain B: N.706, N.707, G.1128, I.1129, V.1130 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: 2 residues within 4Å: Chain B: N.798, S.800 Ligand excluded by PLIP NAG.23: 3 residues within 4Å: Chain B: N.613, T.615, Q.641 Ligand excluded by PLIP NAG.24: 1 residues within 4Å: Chain C: N.654 Ligand excluded by PLIP NAG.25: 2 residues within 4Å: Chain C: N.328, Q.577 Ligand excluded by PLIP NAG.26: 3 residues within 4Å: Chain B: K.459, E.462 Chain C: N.231 Ligand excluded by PLIP NAG.27: 1 residues within 4Å: Chain C: N.600 Ligand excluded by PLIP NAG.28: 2 residues within 4Å: Chain C: E.1069, N.1071 Ligand excluded by PLIP NAG.29: 1 residues within 4Å: Chain C: N.1131 Ligand excluded by PLIP NAG.30: 3 residues within 4Å: Chain C: N.1095, T.1097, F.1100 Ligand excluded by PLIP NAG.31: 2 residues within 4Å: Chain C: N.159, N.160 Ligand excluded by PLIP NAG.32: 3 residues within 4Å: Chain C: N.613, T.615, Q.641 Ligand excluded by PLIP NAG.33: 2 residues within 4Å: Chain A: Y.793 Chain C: N.706 Ligand excluded by PLIP NAG.34: 3 residues within 4Å: Chain C: N.798, S.800, Q.801 Ligand excluded by PLIP NAG.35: 2 residues within 4Å: Chain C: N.277, 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: D
JMB2002 Fab light chian: E
Anti-Fab nanobody: F

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
X

E
Y

F
Z

Spike glycoprotein

JMB2002 Fab heavy chain

JMB2002 Fab light chian

Anti-Fab nanobody

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