SMTL ID : 7wtf.1

SARS-CoV-2 Omicron variant spike in complex with Fab XGv051

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-mer

Ligands

15 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)(Non-covalent)

NAG-NAG.1: 4 residues within 4Å: Chain C: N.701, L.906, Q.910, Q.1055 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 2 residues within 4Å: Chain C: N.785, S.787 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 1 residues within 4Å: Chain C: N.1058 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 1 residues within 4Å: Chain D: N.218 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 2 residues within 4Å: Chain D: N.701, L.906 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 3 residues within 4Å: Chain D: N.785, S.787, Q.788 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 3 residues within 4Å: Chain D: N.264, E.265, N.266 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 4 residues within 4Å: Chain C: Q.879 Chain D: A.690, S.695, N.1058 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 3 residues within 4Å: Chain D: N.315, Q.564, T.565 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:T.565 NAG-NAG.14: 2 residues within 4Å: Chain E: T.93, N.218 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:T.93, E:T.93 NAG-NAG.15: 3 residues within 4Å: Chain E: T.700, N.701, Q.1055 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 2 residues within 4Å: Chain E: A.690, N.1058 No protein-ligand interaction detected (PLIP) NAG-NAG.17: 2 residues within 4Å: Chain E: N.785, S.787 No protein-ligand interaction detected (PLIP) NAG-NAG.19: 1 residues within 4Å: Chain E: N.1118 No protein-ligand interaction detected (PLIP) NAG-NAG.20: 1 residues within 4Å: Chain E: N.315 No protein-ligand interaction detected (PLIP)

5 x NAG- NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA.3: 4 residues within 4Å: Chain C: N.1082, T.1084, H.1085, F.1087 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.4: 1 residues within 4Å: Chain C: N.1118 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.9: 4 residues within 4Å: Chain D: N.1082, T.1084, H.1085, F.1087 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.10: 1 residues within 4Å: Chain D: N.1118 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.18: 4 residues within 4Å: Chain E: N.1082, T.1084, H.1085, F.1087 No protein-ligand interaction detected (PLIP)

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

NAG.21: 2 residues within 4Å: Chain C: Y.1139, N.1142 Ligand excluded by PLIP NAG.22: 4 residues within 4Å: Chain C: C.2, N.4, C.121, N.122 Ligand excluded by PLIP NAG.23: 2 residues within 4Å: Chain C: Y.15, N.48 Ligand excluded by PLIP NAG.24: 1 residues within 4Å: Chain C: N.587 Ligand excluded by PLIP NAG.25: 1 residues within 4Å: Chain C: N.641 Ligand excluded by PLIP NAG.26: 2 residues within 4Å: Chain C: N.600, Q.628 Ligand excluded by PLIP NAG.27: 2 residues within 4Å: Chain C: N.693 Chain E: Y.780 Ligand excluded by PLIP NAG.28: 3 residues within 4Å: Chain C: N.107, V.112, F.139 Ligand excluded by PLIP NAG.29: 3 residues within 4Å: Chain C: N.130, N.131, K.132 Ligand excluded by PLIP NAG.30: 2 residues within 4Å: Chain C: N.315, Q.564 Ligand excluded by PLIP NAG.31: 3 residues within 4Å: Chain C: N.264, N.266 Chain D: K.542 Ligand excluded by PLIP NAG.32: 4 residues within 4Å: Chain D: Y.1139, N.1142 Chain E: K.1141, T.1144 Ligand excluded by PLIP NAG.33: 3 residues within 4Å: Chain D: A.108, T.109, N.110 Ligand excluded by PLIP NAG.34: 5 residues within 4Å: Chain D: C.2, V.3, N.4, C.121, D.123 Ligand excluded by PLIP NAG.35: 2 residues within 4Å: Chain D: Y.15, N.48 Ligand excluded by PLIP NAG.36: 1 residues within 4Å: Chain D: N.587 Ligand excluded by PLIP NAG.37: 1 residues within 4Å: Chain D: N.641 Ligand excluded by PLIP NAG.38: 2 residues within 4Å: Chain C: Y.780 Chain D: N.693 Ligand excluded by PLIP NAG.39: 2 residues within 4Å: Chain D: N.130, N.131 Ligand excluded by PLIP NAG.40: 1 residues within 4Å: Chain D: N.147 Ligand excluded by PLIP NAG.41: 1 residues within 4Å: Chain D: N.600 Ligand excluded by PLIP NAG.42: 3 residues within 4Å: Chain C: T.1144 Chain E: Y.1139, N.1142 Ligand excluded by PLIP NAG.43: 2 residues within 4Å: Chain E: C.2, N.4 Ligand excluded by PLIP NAG.44: 2 residues within 4Å: Chain E: Y.15, N.48 Ligand excluded by PLIP NAG.45: 1 residues within 4Å: Chain E: N.587 Ligand excluded by PLIP NAG.46: 1 residues within 4Å: Chain E: N.641 Ligand excluded by PLIP NAG.47: 2 residues within 4Å: Chain D: Y.780 Chain E: N.693 Ligand excluded by PLIP NAG.48: 2 residues within 4Å: Chain E: N.131, K.132 Ligand excluded by PLIP NAG.49: 2 residues within 4Å: Chain E: N.264, N.266 Ligand excluded by PLIP NAG.50: 1 residues within 4Å: Chain E: N.600 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, L. et al., Selection and structural bases of potent broadly neutralizing antibodies from 3-dose vaccinees that are highly effective against diverse SARS-CoV-2 variants, including Omicron sublineages. Cell Res. (2022)

Release Date

2022-12-14

Peptides

Heavy chain of XGv051: AFH
Light chain of XGv051: BGI
Spike glycoprotein: CDE

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
H

F
G

H
I

B
L

G
J

I
K

C
B

D
C

E
D

Heavy chain of XGv051

Light chain of XGv051

Spike glycoprotein

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