SMTL ID : 7web.1

SARS-CoV-2 Omicron variant spike protein with two XGv347 binding to two open state RBDs

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-2-3-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: 6 residues within 4Å: Chain E: F.326, N.328, I.329, Q.577, T.578, L.579 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 2 residues within 4Å: Chain E: N.714, Q.923 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 5 residues within 4Å: Chain E: A.703, S.705, N.707, S.708, N.1071 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:N.1071 NAG-NAG.4: 2 residues within 4Å: Chain E: N.798, S.800 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 2 residues within 4Å: Chain F: N.231, T.233 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 4 residues within 4Å: Chain F: N.328, P.576, Q.577, L.579 1 PLIP interactions: 1 interactions with chain F Hydrophobic interactions: F:L.579 NAG-NAG.9: 2 residues within 4Å: Chain F: N.714, Q.923 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 3 residues within 4Å: Chain F: A.703, S.705, N.1071 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:N.1071 NAG-NAG.11: 2 residues within 4Å: Chain F: N.798, S.800 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 2 residues within 4Å: Chain G: T.106, N.231 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 3 residues within 4Å: Chain G: N.328, I.329, Q.577 1 PLIP interactions: 1 interactions with chain G Hydrogen bonds: G:N.328 NAG-NAG.16: 3 residues within 4Å: Chain G: N.714, L.919, Q.1068 No protein-ligand interaction detected (PLIP) NAG-NAG.17: 1 residues within 4Å: Chain G: N.1071 No protein-ligand interaction detected (PLIP) NAG-NAG.18: 3 residues within 4Å: Chain G: N.798, S.800, Q.801 No protein-ligand interaction detected (PLIP) NAG-NAG.20: 1 residues within 4Å: Chain G: N.1131 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.5: 4 residues within 4Å: Chain E: N.1095, T.1097, H.1098, F.1100 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.6: 1 residues within 4Å: Chain E: N.1131 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.12: 4 residues within 4Å: Chain F: N.1095, T.1097, H.1098, F.1100 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.13: 1 residues within 4Å: Chain F: N.1131 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.19: 4 residues within 4Å: Chain G: N.1095, T.1097, H.1098, F.1100 No protein-ligand interaction detected (PLIP)

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

NAG.21: 2 residues within 4Å: Chain E: Y.1152, N.1155 Ligand excluded by PLIP NAG.22: 4 residues within 4Å: Chain E: N.120, A.121, T.122, N.123 Ligand excluded by PLIP NAG.23: 3 residues within 4Å: Chain E: K.142, N.143, S.251 Ligand excluded by PLIP NAG.24: 5 residues within 4Å: Chain E: C.15, V.16, N.17, C.134, N.135 Ligand excluded by PLIP NAG.25: 1 residues within 4Å: Chain E: N.61 Ligand excluded by PLIP NAG.26: 2 residues within 4Å: Chain E: E.306, N.600 Ligand excluded by PLIP NAG.27: 1 residues within 4Å: Chain E: N.654 Ligand excluded by PLIP NAG.28: 3 residues within 4Å: Chain E: N.613, C.614, Q.641 Ligand excluded by PLIP NAG.29: 1 residues within 4Å: Chain E: N.706 Ligand excluded by PLIP NAG.30: 6 residues within 4Å: Chain E: T.112, I.230 Chain F: R.463, D.464, I.465 Ligands: NAG.31 Ligand excluded by PLIP NAG.31: 11 residues within 4Å: Chain F: Y.348, W.350, R.451, R.454, E.462, R.463, D.464, I.465, S.466, Y.470 Ligands: NAG.30 Ligand excluded by PLIP NAG.32: 2 residues within 4Å: Chain F: Y.1152, N.1155 Ligand excluded by PLIP NAG.33: 4 residues within 4Å: Chain F: N.120, A.121, T.122, N.123 Ligand excluded by PLIP NAG.34: 3 residues within 4Å: Chain F: K.142, N.143, S.251 Ligand excluded by PLIP NAG.35: 4 residues within 4Å: Chain F: C.15, V.16, N.17, N.135 Ligand excluded by PLIP NAG.36: 3 residues within 4Å: Chain F: Y.28, N.30, N.61 Ligand excluded by PLIP NAG.37: 2 residues within 4Å: Chain F: N.600, T.601 Ligand excluded by PLIP NAG.38: 1 residues within 4Å: Chain F: N.654 Ligand excluded by PLIP NAG.39: 3 residues within 4Å: Chain F: N.613, C.614, Q.641 Ligand excluded by PLIP NAG.40: 1 residues within 4Å: Chain F: N.706 Ligand excluded by PLIP NAG.41: 1 residues within 4Å: Chain G: G.229 Ligand excluded by PLIP NAG.42: 2 residues within 4Å: Chain G: K.1151, N.1155 Ligand excluded by PLIP NAG.43: 2 residues within 4Å: Chain G: N.143, S.251 Ligand excluded by PLIP NAG.44: 4 residues within 4Å: Chain G: C.15, V.16, N.17, C.134 Ligand excluded by PLIP NAG.45: 2 residues within 4Å: Chain G: Y.28, N.61 Ligand excluded by PLIP NAG.46: 1 residues within 4Å: Chain G: N.600 Ligand excluded by PLIP NAG.47: 1 residues within 4Å: Chain G: N.654 Ligand excluded by PLIP NAG.48: 3 residues within 4Å: Chain G: N.613, C.614, Q.641 Ligand excluded by PLIP NAG.49: 1 residues within 4Å: Chain G: 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

The heavy chain of Fab XGv347: AB
The light chain of Fab XGv347: CD
Spike glycoprotein: EFG

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
G

B
H

C
I

D
L

E
B

F
C

G
D

The heavy chain of Fab XGv347

The light chain of Fab XGv347

Spike glycoprotein

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