SMTL ID : 7wea.1

SARS-CoV-2 Omicron variant spike protein in complex with two XGv347 binding to one close state RBD and one open state RBD

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-2-2-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: 3 residues within 4Å: Chain A: T.106, N.231, T.233 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 5 residues within 4Å: Chain A: P.327, N.328, P.576, Q.577, T.578 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 4 residues within 4Å: Chain A: N.714, L.919, Q.923, Q.1068 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.919 NAG-NAG.4: 3 residues within 4Å: Chain A: A.703, S.708, N.1071 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 3 residues within 4Å: Chain A: N.798, S.800, Q.801 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: 2 residues within 4Å: Chain B: I.329, Q.577 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 4 residues within 4Å: Chain B: N.714, L.919, Q.923, Q.1068 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 5 residues within 4Å: Chain B: A.703, Y.704, S.705, S.708, N.1071 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.1071 NAG-NAG.11: 2 residues within 4Å: Chain B: N.798, S.800 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 8 residues within 4Å: Chain A: R.451, R.454, E.462, R.463, D.464, I.465, S.466 Chain C: N.231 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.451, A:R.451, A:R.454, A:S.466 NAG-NAG.15: 5 residues within 4Å: Chain C: N.328, P.576, Q.577, T.578, L.579 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:L.579 Hydrogen bonds: C:T.578 NAG-NAG.16: 2 residues within 4Å: Chain C: N.714, Q.923 No protein-ligand interaction detected (PLIP) NAG-NAG.17: 3 residues within 4Å: Chain C: S.705, S.708, N.1071 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.1071 NAG-NAG.18: 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: 3 residues within 4Å: Chain A: N.1095, H.1098, F.1100 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.12: 2 residues within 4Å: Chain B: N.1095, H.1098 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.13: 1 residues within 4Å: Chain B: N.1131 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.19: 4 residues within 4Å: Chain C: N.1095, T.1097, H.1098, F.1100 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.20: 1 residues within 4Å: Chain C: N.1131 No protein-ligand interaction detected (PLIP)

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

NAG.21: 1 residues within 4Å: Chain A: G.229 Ligand excluded by PLIP NAG.22: 3 residues within 4Å: Chain A: K.1151, Y.1152, N.1155 Ligand excluded by PLIP NAG.23: 2 residues within 4Å: Chain A: N.143, S.251 Ligand excluded by PLIP NAG.24: 5 residues within 4Å: Chain A: C.15, V.16, N.17, C.134, N.135 Ligand excluded by PLIP NAG.25: 3 residues within 4Å: Chain A: Y.28, N.61, V.62 Ligand excluded by PLIP NAG.26: 1 residues within 4Å: Chain A: N.600 Ligand excluded by PLIP NAG.27: 1 residues within 4Å: Chain A: N.654 Ligand excluded by PLIP NAG.28: 2 residues within 4Å: Chain A: N.613, Q.641 Ligand excluded by PLIP NAG.29: 1 residues within 4Å: Chain A: N.706 Ligand excluded by PLIP NAG.30: 3 residues within 4Å: Chain B: K.1151, Y.1152, N.1155 Ligand excluded by PLIP NAG.31: 4 residues within 4Å: Chain B: N.120, A.121, T.122, N.123 Ligand excluded by PLIP NAG.32: 3 residues within 4Å: Chain B: K.142, N.143, S.251 Ligand excluded by PLIP NAG.33: 2 residues within 4Å: Chain B: C.15, N.17 Ligand excluded by PLIP NAG.34: 1 residues within 4Å: Chain B: N.61 Ligand excluded by PLIP NAG.35: 3 residues within 4Å: Chain B: G.598, N.600, T.601 Ligand excluded by PLIP NAG.36: 2 residues within 4Å: Chain B: Y.652, N.654 Ligand excluded by PLIP NAG.37: 3 residues within 4Å: Chain B: N.613, T.615, Q.641 Ligand excluded by PLIP NAG.38: 1 residues within 4Å: Chain B: N.706 Ligand excluded by PLIP NAG.39: 6 residues within 4Å: Chain B: T.106, I.230 Chain C: F.461, E.462, R.463 Ligands: NAG.40 Ligand excluded by PLIP NAG.40: 5 residues within 4Å: Chain C: R.463, D.464, I.465, S.466 Ligands: NAG.39 Ligand excluded by PLIP NAG.41: 1 residues within 4Å: Chain C: N.1155 Ligand excluded by PLIP NAG.42: 4 residues within 4Å: Chain C: N.120, A.121, T.122, N.123 Ligand excluded by PLIP NAG.43: 3 residues within 4Å: Chain C: K.142, N.143, S.251 Ligand excluded by PLIP NAG.44: 5 residues within 4Å: Chain C: C.15, V.16, N.17, N.135, D.136 Ligand excluded by PLIP NAG.45: 2 residues within 4Å: Chain C: Y.28, N.61 Ligand excluded by PLIP NAG.46: 2 residues within 4Å: Chain C: E.306, N.600 Ligand excluded by PLIP NAG.47: 1 residues within 4Å: Chain C: N.654 Ligand excluded by PLIP NAG.48: 2 residues within 4Å: Chain C: N.613, Q.641 Ligand excluded by PLIP NAG.49: 1 residues within 4Å: 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
The heavy chain of Fab XGv347: DF
The light chain of Fab XGv347: EG

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
H

F
G

E
L

G
I

Spike glycoprotein

The heavy chain of Fab XGv347

The light chain of Fab XGv347

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