SMTL ID : 7yvn.1

Omicron BA.4/5 SARS-CoV-2 S in complex with TH281 Fab

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-mer

Ligands

36 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Non-functional Binders)(Non-covalent)

NAG.1: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP NAG.2: 3 residues within 4Å: Chain A: D.111, S.112, K.113 Ligand excluded by PLIP NAG.3: 2 residues within 4Å: Chain A: E.281, N.282 Ligand excluded by PLIP NAG.4: 3 residues within 4Å: Chain A: Y.796 Chain B: N.709 Ligands: NAG.23 Ligand excluded by PLIP NAG.5: 3 residues within 4Å: Chain A: N.709 Chain C: Y.796 Ligands: NAG.12 Ligand excluded by PLIP NAG.6: 1 residues within 4Å: Chain A: N.657 Ligand excluded by PLIP NAG.7: 1 residues within 4Å: Chain A: N.603 Ligand excluded by PLIP NAG.8: 1 residues within 4Å: Chain A: N.1074 Ligand excluded by PLIP NAG.9: 2 residues within 4Å: Chain A: I.1132, N.1134 Ligand excluded by PLIP NAG.10: 4 residues within 4Å: Chain A: N.1098, T.1100, H.1101, F.1103 Ligand excluded by PLIP NAG.11: 1 residues within 4Å: Chain A: N.616 Ligand excluded by PLIP NAG.12: 4 residues within 4Å: Chain A: S.708, N.709, N.710 Ligands: NAG.5 Ligand excluded by PLIP NAG.13: 2 residues within 4Å: Chain A: N.801, Q.804 Ligand excluded by PLIP NAG.14: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP NAG.15: 1 residues within 4Å: Chain B: K.113 Ligand excluded by PLIP NAG.16: 3 residues within 4Å: Chain B: N.280, E.281, N.282 Ligand excluded by PLIP NAG.17: 1 residues within 4Å: Chain B: N.657 Ligand excluded by PLIP NAG.18: 1 residues within 4Å: Chain B: N.603 Ligand excluded by PLIP NAG.19: 3 residues within 4Å: Chain B: A.706, E.1072, N.1074 Ligand excluded by PLIP NAG.20: 1 residues within 4Å: Chain B: N.1134 Ligand excluded by PLIP NAG.21: 3 residues within 4Å: Chain B: N.1098, T.1100, H.1101 Ligand excluded by PLIP NAG.22: 1 residues within 4Å: Chain B: N.616 Ligand excluded by PLIP NAG.23: 4 residues within 4Å: Chain B: S.708, N.709, N.710 Ligands: NAG.4 Ligand excluded by PLIP NAG.24: 2 residues within 4Å: Chain B: N.801, S.803 Ligand excluded by PLIP NAG.25: 3 residues within 4Å: Chain B: Y.796 Chain C: N.709 Ligands: NAG.32 Ligand excluded by PLIP NAG.26: 1 residues within 4Å: Chain C: N.657 Ligand excluded by PLIP NAG.27: 1 residues within 4Å: Chain C: N.603 Ligand excluded by PLIP NAG.28: 2 residues within 4Å: Chain B: Q.895 Chain C: N.1074 Ligand excluded by PLIP NAG.29: 1 residues within 4Å: Chain C: N.1134 Ligand excluded by PLIP NAG.30: 3 residues within 4Å: Chain C: N.1098, T.1100, H.1101 Ligand excluded by PLIP NAG.31: 2 residues within 4Å: Chain C: N.616, Q.644 Ligand excluded by PLIP NAG.32: 4 residues within 4Å: Chain C: S.708, N.709, N.710 Ligands: NAG.25 Ligand excluded by PLIP NAG.33: 2 residues within 4Å: Chain C: N.801, S.803 Ligand excluded by PLIP NAG.34: 1 residues within 4Å: Chain C: N.234 Ligand excluded by PLIP NAG.35: 1 residues within 4Å: Chain C: N.165 Ligand excluded by PLIP NAG.36: 2 residues within 4Å: Chain C: E.281, N.282 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Guo, Y. et al., Discovery and characterization of potent pan-variant SARS-CoV-2 neutralizing antibodies from individuals with Omicron breakthrough infection. Nat Commun (2023)

Release Date

2023-06-28

Peptides

Spike glycoprotein: ABC
TH281 Fab light chain: DFH
TH281 Fab heavy chain: EGI

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
B

C
A

D
H

F
K

H
N

E
I

G
L

I
O

Spike glycoprotein

TH281 Fab light chain

TH281 Fab heavy chain

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