SMTL ID : 7yvo.1

Omicron BA.4/5 SARS-CoV-2 S in complex with TH027/132 Fab

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-2-2-2-2-mer

Ligands

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

NAG.1: 3 residues within 4Å: Chain A: G.232, I.233, N.234 Ligand excluded by PLIP NAG.2: 3 residues within 4Å: Chain A: Q.115, E.132, N.165 Ligand excluded by PLIP NAG.3: 2 residues within 4Å: Chain A: N.280, N.282 Ligand excluded by PLIP NAG.4: 3 residues within 4Å: Chain A: N.709 Chain B: Y.796 Ligands: NAG.11 Ligand excluded by PLIP NAG.5: 1 residues within 4Å: Chain A: N.657 Ligand excluded by PLIP NAG.6: 1 residues within 4Å: Chain A: N.603 Ligand excluded by PLIP NAG.7: 1 residues within 4Å: Chain A: N.1074 Ligand excluded by PLIP NAG.8: 1 residues within 4Å: Chain A: N.1134 Ligand excluded by PLIP NAG.9: 3 residues within 4Å: Chain A: N.1098, T.1100, H.1101 Ligand excluded by PLIP NAG.10: 1 residues within 4Å: Chain A: N.616 Ligand excluded by PLIP NAG.11: 4 residues within 4Å: Chain A: S.708, N.709 Chain B: I.794 Ligands: NAG.4 Ligand excluded by PLIP NAG.12: 2 residues within 4Å: Chain A: N.801, S.803 Ligand excluded by PLIP NAG.13: 3 residues within 4Å: Chain B: T.108, N.234, T.236 Ligand excluded by PLIP NAG.14: 6 residues within 4Å: Chain B: S.112, K.113, T.114, E.132, A.163, N.165 Ligand excluded by PLIP NAG.15: 3 residues within 4Å: Chain B: N.280, E.281, N.282 Ligand excluded by PLIP NAG.16: 1 residues within 4Å: Chain B: N.657 Ligand excluded by PLIP NAG.17: 4 residues within 4Å: Chain B: R.328, N.331, Q.580, T.581 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: 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: 3 residues within 4Å: Chain B: N.709, N.710 Ligands: NAG.25 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: N.709 Chain C: Y.796 Ligands: NAG.23 Ligand excluded by PLIP NAG.26: 4 residues within 4Å: Chain A: I.794, Y.796 Chain C: N.709 Ligands: NAG.33 Ligand excluded by PLIP NAG.27: 1 residues within 4Å: Chain C: N.657 Ligand excluded by PLIP NAG.28: 1 residues within 4Å: Chain C: N.603 Ligand excluded by PLIP NAG.29: 1 residues within 4Å: Chain C: N.1074 Ligand excluded by PLIP NAG.30: 1 residues within 4Å: Chain C: N.1134 Ligand excluded by PLIP NAG.31: 3 residues within 4Å: Chain C: N.1098, T.1100, H.1101 Ligand excluded by PLIP NAG.32: 2 residues within 4Å: Chain C: N.616, Q.644 Ligand excluded by PLIP NAG.33: 2 residues within 4Å: Chain C: N.709 Ligands: NAG.26 Ligand excluded by PLIP NAG.34: 1 residues within 4Å: Chain C: N.801 Ligand excluded by PLIP NAG.35: 2 residues within 4Å: Chain C: T.108, N.234 Ligand excluded by PLIP NAG.36: 3 residues within 4Å: Chain C: S.112, K.113, N.165 Ligand excluded by PLIP NAG.37: 3 residues within 4Å: Chain C: N.280, 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
TH132 Fab light chain: DF
TH132 Fab heavy chain: EG
TH27 Fab light chain: HJ
TH27 Fab heavy chain: IK

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
H

F
J

E
I

G
K

H
L

J
N

I
M

K
O

Spike glycoprotein

TH132 Fab light chain

TH132 Fab heavy chain

TH27 Fab light chain

TH27 Fab heavy chain

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