SMTL ID : 7we8.1

SARS-CoV-2 Omicron variant spike protein in complex with Fab XGv265

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-1-1-mer

Ligands

14 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: 2 residues within 4Å: Chain A: T.106, N.231 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 2 residues within 4Å: Chain A: N.328, I.329 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 2 residues within 4Å: Chain A: N.714, L.919 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 1 residues within 4Å: Chain A: N.1071 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 2 residues within 4Å: Chain A: N.798, S.800 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 1 residues within 4Å: Chain A: N.1131 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 1 residues within 4Å: Chain B: N.714 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 4 residues within 4Å: Chain B: S.705, N.707, S.708, N.1071 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.1071 NAG-NAG.10: 3 residues within 4Å: Chain B: N.798, S.800, Q.801 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 2 residues within 4Å: Chain B: N.328, Q.577 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 3 residues within 4Å: Chain C: N.328, P.576, Q.577 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:Q.577 NAG-NAG.15: 2 residues within 4Å: Chain C: N.714, L.919 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 2 residues within 4Å: Chain C: S.705, N.1071 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.1071 NAG-NAG.17: 2 residues within 4Å: Chain C: N.798, S.800 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.6: 4 residues within 4Å: Chain A: N.1095, T.1097, H.1098, F.1100 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.11: 4 residues within 4Å: Chain B: N.1095, T.1097, H.1098, F.1100 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.12: 1 residues within 4Å: Chain B: N.1131 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.18: 4 residues within 4Å: Chain C: N.1095, T.1097, H.1098, F.1100 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.19: 1 residues within 4Å: Chain C: N.1131 No protein-ligand interaction detected (PLIP)

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

NAG.20: 2 residues within 4Å: Chain A: Y.1152, N.1155 Ligand excluded by PLIP NAG.21: 2 residues within 4Å: Chain A: N.143, S.251 Ligand excluded by PLIP NAG.22: 3 residues within 4Å: Chain A: C.15, N.17, C.134 Ligand excluded by PLIP NAG.23: 2 residues within 4Å: Chain A: Y.28, N.61 Ligand excluded by PLIP NAG.24: 1 residues within 4Å: Chain A: N.600 Ligand excluded by PLIP NAG.25: 2 residues within 4Å: Chain A: Y.652, N.654 Ligand excluded by PLIP NAG.26: 2 residues within 4Å: Chain A: N.613, Q.641 Ligand excluded by PLIP NAG.27: 2 residues within 4Å: Chain A: N.706, N.707 Ligand excluded by PLIP NAG.28: 3 residues within 4Å: Chain B: K.1151, Y.1152, N.1155 Ligand excluded by PLIP NAG.29: 6 residues within 4Å: Chain B: N.120, A.121, N.123, E.149, F.152, R.153 Ligand excluded by PLIP NAG.30: 3 residues within 4Å: Chain B: K.142, N.143, N.144 Ligand excluded by PLIP NAG.31: 3 residues within 4Å: Chain B: C.15, V.16, N.17 Ligand excluded by PLIP NAG.32: 1 residues within 4Å: Chain B: N.61 Ligand excluded by PLIP NAG.33: 2 residues within 4Å: Chain B: N.600, T.601 Ligand excluded by PLIP NAG.34: 1 residues within 4Å: Chain B: N.654 Ligand excluded by PLIP NAG.35: 3 residues within 4Å: Chain B: N.613, C.614, Q.641 Ligand excluded by PLIP NAG.36: 2 residues within 4Å: Chain A: Y.793 Chain B: N.706 Ligand excluded by PLIP NAG.37: 3 residues within 4Å: Chain C: K.1151, Y.1152, N.1155 Ligand excluded by PLIP NAG.38: 4 residues within 4Å: Chain C: N.120, A.121, T.122, N.123 Ligand excluded by PLIP NAG.39: 3 residues within 4Å: Chain C: K.142, N.143, S.251 Ligand excluded by PLIP NAG.40: 5 residues within 4Å: Chain C: C.15, V.16, N.17, N.135, D.136 Ligand excluded by PLIP NAG.41: 2 residues within 4Å: Chain C: Y.28, N.61 Ligand excluded by PLIP NAG.42: 3 residues within 4Å: Chain C: G.598, N.600, T.601 Ligand excluded by PLIP NAG.43: 1 residues within 4Å: Chain C: N.654 Ligand excluded by PLIP NAG.44: 3 residues within 4Å: Chain C: N.613, C.614, Q.641 Ligand excluded by PLIP NAG.45: 2 residues within 4Å: Chain B: Y.793 Chain C: N.706 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, K. et al., Memory B cell repertoire from triple vaccinees against diverse SARS-CoV-2 variants. Nature (2022)

Release Date

2022-05-04

Peptides

Spike glycoprotein: ABC
Heavy chain of Fab 265: D
Light chain of Fab 265: E

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
H

E
L

Spike glycoprotein

Heavy chain of Fab 265

Light chain of Fab 265

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