SMTL ID : 8gtp.1

cryo-EM structure of Omicron BA.5 S protein in complex with XGv289

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-mer

Ligands

18 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: 1 residues within 4Å: Chain A: N.329 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 3 residues within 4Å: Chain A: N.341, N.368, F.369 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 3 residues within 4Å: Chain A: N.715, L.920, Q.924 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.920 NAG-NAG.4: 3 residues within 4Å: Chain A: N.799, S.801, Q.802 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 3 residues within 4Å: Chain A: N.1096, T.1098, H.1099 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 1 residues within 4Å: Chain A: N.1132 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 3 residues within 4Å: Chain B: N.329, Q.578, L.580 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 3 residues within 4Å: Chain B: N.341, N.368, F.369 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 3 residues within 4Å: Chain B: N.715, L.920, Q.924 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:L.920 NAG-NAG.10: 3 residues within 4Å: Chain B: N.799, S.801, Q.802 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 3 residues within 4Å: Chain B: N.1096, T.1098, H.1099 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 1 residues within 4Å: Chain B: N.1132 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 3 residues within 4Å: Chain C: N.329, Q.578, L.580 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 3 residues within 4Å: Chain C: N.341, N.368, F.369 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 3 residues within 4Å: Chain C: N.715, L.920, Q.924 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:L.920 NAG-NAG.16: 3 residues within 4Å: Chain C: N.799, S.801, Q.802 No protein-ligand interaction detected (PLIP) NAG-NAG.17: 3 residues within 4Å: Chain C: N.1096, T.1098, H.1099 No protein-ligand interaction detected (PLIP) NAG-NAG.18: 1 residues within 4Å: Chain C: N.1132 No protein-ligand interaction detected (PLIP)

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

NAG.19: 2 residues within 4Å: Chain A: F.59, N.61 Ligand excluded by PLIP NAG.20: 3 residues within 4Å: Chain A: N.120, N.123, V.125 Ligand excluded by PLIP NAG.21: 3 residues within 4Å: Chain A: Q.113, E.130, N.163 Ligand excluded by PLIP NAG.22: 1 residues within 4Å: Chain A: N.232 Ligand excluded by PLIP NAG.23: 1 residues within 4Å: Chain A: N.280 Ligand excluded by PLIP NAG.24: 1 residues within 4Å: Chain A: N.601 Ligand excluded by PLIP NAG.25: 3 residues within 4Å: Chain A: N.614, T.616, Q.642 Ligand excluded by PLIP NAG.26: 2 residues within 4Å: Chain A: Y.653, N.655 Ligand excluded by PLIP NAG.27: 1 residues within 4Å: Chain A: N.707 Ligand excluded by PLIP NAG.28: 4 residues within 4Å: Chain A: A.704, E.1070, N.1072 Ligands: NAG.29 Ligand excluded by PLIP NAG.29: 1 residues within 4Å: Ligands: NAG.28 Ligand excluded by PLIP NAG.30: 2 residues within 4Å: Chain B: F.59, N.61 Ligand excluded by PLIP NAG.31: 3 residues within 4Å: Chain B: N.120, N.123, V.125 Ligand excluded by PLIP NAG.32: 3 residues within 4Å: Chain B: Q.113, E.130, N.163 Ligand excluded by PLIP NAG.33: 4 residues within 4Å: Chain A: K.460, E.463, R.464 Chain B: N.232 Ligand excluded by PLIP NAG.34: 1 residues within 4Å: Chain B: N.280 Ligand excluded by PLIP NAG.35: 1 residues within 4Å: Chain B: N.601 Ligand excluded by PLIP NAG.36: 3 residues within 4Å: Chain B: N.614, T.616, Q.642 Ligand excluded by PLIP NAG.37: 2 residues within 4Å: Chain B: Y.653, N.655 Ligand excluded by PLIP NAG.38: 1 residues within 4Å: Chain B: N.707 Ligand excluded by PLIP NAG.39: 4 residues within 4Å: Chain B: A.704, E.1070, N.1072 Ligands: NAG.40 Ligand excluded by PLIP NAG.40: 1 residues within 4Å: Ligands: NAG.39 Ligand excluded by PLIP NAG.41: 2 residues within 4Å: Chain C: F.59, N.61 Ligand excluded by PLIP NAG.42: 3 residues within 4Å: Chain C: N.120, N.123, V.125 Ligand excluded by PLIP NAG.43: 3 residues within 4Å: Chain C: Q.113, E.130, N.163 Ligand excluded by PLIP NAG.44: 1 residues within 4Å: Chain C: N.232 Ligand excluded by PLIP NAG.45: 1 residues within 4Å: Chain C: N.280 Ligand excluded by PLIP NAG.46: 1 residues within 4Å: Chain C: N.601 Ligand excluded by PLIP NAG.47: 3 residues within 4Å: Chain C: N.614, T.616, Q.642 Ligand excluded by PLIP NAG.48: 2 residues within 4Å: Chain C: Y.653, N.655 Ligand excluded by PLIP NAG.49: 1 residues within 4Å: Chain C: N.707 Ligand excluded by PLIP NAG.50: 4 residues within 4Å: Chain C: A.704, E.1070, N.1072 Ligands: NAG.51 Ligand excluded by PLIP NAG.51: 1 residues within 4Å: Ligands: NAG.50 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chi, X. et al., Comprehensive structural analysis reveals broad-spectrum neutralizing antibodies against SARS-CoV-2 Omicron variants. Cell Discov (2023)

Release Date

2023-07-12

Peptides

Spike glycoprotein: ABC
heavy chain of XGv289: DFH
light chain of XGv289: EGI

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
H

F
I

H
J

E
L

G
M

I
N

Spike glycoprotein

heavy chain of XGv289

light chain of XGv289

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