SMTL ID : 7yve.1

Omicron BA.4/5 SARS-CoV-2 S in complex with TH027 Fab

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-mer

Ligands

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

NAG.1: 1 residues within 4Å: Chain A: N.657 Ligand excluded by PLIP NAG.2: 1 residues within 4Å: Chain A: N.603 Ligand excluded by PLIP NAG.3: 1 residues within 4Å: Chain A: N.1074 Ligand excluded by PLIP NAG.4: 1 residues within 4Å: Chain A: N.1134 Ligand excluded by PLIP NAG.5: 3 residues within 4Å: Chain A: N.1098, T.1100, H.1101 Ligand excluded by PLIP NAG.6: 2 residues within 4Å: Chain A: N.616, Q.644 Ligand excluded by PLIP NAG.7: 2 residues within 4Å: Chain A: N.709 Ligands: NAG.25 Ligand excluded by PLIP NAG.8: 2 residues within 4Å: Chain A: N.801, S.803 Ligand excluded by PLIP NAG.9: 1 residues within 4Å: Chain A: N.234 Ligand excluded by PLIP NAG.10: 3 residues within 4Å: Chain A: S.112, K.113, N.165 Ligand excluded by PLIP NAG.11: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP NAG.12: 3 residues within 4Å: Chain A: Y.796 Chain B: N.709 Ligands: NAG.23 Ligand excluded by PLIP NAG.13: 2 residues within 4Å: Chain B: N.234, T.236 Ligand excluded by PLIP NAG.14: 3 residues within 4Å: Chain B: S.112, K.113, N.165 Ligand excluded by PLIP NAG.15: 2 residues within 4Å: Chain B: E.281, N.282 Ligand excluded by PLIP NAG.16: 2 residues within 4Å: Chain B: Y.655, N.657 Ligand excluded by PLIP NAG.17: 1 residues within 4Å: Chain B: N.331 Ligand excluded by PLIP NAG.18: 1 residues within 4Å: Chain B: N.603 Ligand excluded by PLIP NAG.19: 1 residues within 4Å: Chain B: N.1074 Ligand excluded by PLIP NAG.20: 2 residues within 4Å: Chain B: I.1132, 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: 2 residues within 4Å: Chain B: N.616, Q.644 Ligand excluded by PLIP NAG.23: 4 residues within 4Å: Chain B: S.708, N.709, N.710 Ligands: NAG.12 Ligand excluded by PLIP NAG.24: 1 residues within 4Å: Chain B: N.801 Ligand excluded by PLIP NAG.25: 4 residues within 4Å: Chain A: N.709, I.1130 Chain C: Y.796 Ligands: NAG.7 Ligand excluded by PLIP NAG.26: 3 residues within 4Å: Chain B: Y.796 Chain C: N.709 Ligands: NAG.36 Ligand excluded by PLIP NAG.27: 3 residues within 4Å: Chain C: T.108, N.234, T.236 Ligand excluded by PLIP NAG.28: 4 residues within 4Å: Chain C: S.112, A.163, N.164, N.165 Ligand excluded by PLIP NAG.29: 2 residues within 4Å: Chain C: E.281, N.282 Ligand excluded by PLIP NAG.30: 2 residues within 4Å: Chain C: Y.655, N.657 Ligand excluded by PLIP NAG.31: 1 residues within 4Å: Chain C: N.603 Ligand excluded by PLIP NAG.32: 2 residues within 4Å: Chain C: A.706, N.1074 Ligand excluded by PLIP NAG.33: 1 residues within 4Å: Chain C: N.1134 Ligand excluded by PLIP NAG.34: 3 residues within 4Å: Chain C: N.1098, T.1100, H.1101 Ligand excluded by PLIP NAG.35: 2 residues within 4Å: Chain C: N.616, Q.644 Ligand excluded by PLIP NAG.36: 3 residues within 4Å: Chain C: S.708, N.709 Ligands: NAG.26 Ligand excluded by PLIP NAG.37: 3 residues within 4Å: Chain C: N.801, S.803, Q.804 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
TH027 Fab light chain: DFH
TH027 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

TH027 Fab light chain

TH027 Fab heavy chain

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