SMTL ID : 7wec.1

SARS-CoV-2 Omicron variant spike protein with three XGv347 Fabs binding to three closed state RBDs

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-mer

Ligands

16 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: 7 residues within 4Å: Chain G: T.106, N.231 Chain H: R.454, K.455, L.458, K.459, E.462 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 5 residues within 4Å: Chain G: P.327, N.328, P.576, Q.577, T.578 1 PLIP interactions: 1 interactions with chain G Hydrogen bonds: G:T.578 NAG-NAG.3: 3 residues within 4Å: Chain G: N.714, L.919, Q.1068 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 2 residues within 4Å: Chain G: A.703, N.1071 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 4 residues within 4Å: Chain G: N.798, S.800, Q.801, F.814 1 PLIP interactions: 1 interactions with chain G Hydrophobic interactions: G:F.814 NAG-NAG.7: 1 residues within 4Å: Chain G: N.1131 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 13 residues within 4Å: Chain I: V.347, Y.348, A.349, W.350, Y.418, N.419, R.451, L.458, F.461, E.462, R.463, D.464, I.465 4 PLIP interactions: 4 interactions with chain I Hydrophobic interactions: I:W.350 Hydrogen bonds: I:W.350, I:N.419, I:R.451 NAG-NAG.9: 3 residues within 4Å: Chain H: N.328, Q.577, L.579 1 PLIP interactions: 1 interactions with chain H Hydrophobic interactions: H:L.579 NAG-NAG.10: 5 residues within 4Å: Chain H: N.714, F.715, L.919, Q.923, Q.1068 1 PLIP interactions: 1 interactions with chain H Hydrophobic interactions: H:Q.923 NAG-NAG.11: 3 residues within 4Å: Chain H: S.705, S.708, N.1071 1 PLIP interactions: 1 interactions with chain H Hydrogen bonds: H:N.1071 NAG-NAG.12: 4 residues within 4Å: Chain H: N.798, S.800, Q.801, F.814 1 PLIP interactions: 1 interactions with chain H Hydrophobic interactions: H:F.814 NAG-NAG.15: 10 residues within 4Å: Chain G: Y.348, R.451, R.454, E.462, R.463, D.464, I.465, S.466 Chain I: N.231, T.233 4 PLIP interactions: 4 interactions with chain G Hydrogen bonds: G:R.451, G:R.454, G:S.466, G:S.466 NAG-NAG.16: 4 residues within 4Å: Chain I: N.328, P.576, Q.577, L.579 1 PLIP interactions: 1 interactions with chain I Hydrophobic interactions: I:L.579 NAG-NAG.17: 3 residues within 4Å: Chain I: N.714, L.919, Q.1068 No protein-ligand interaction detected (PLIP) NAG-NAG.18: 4 residues within 4Å: Chain I: S.705, N.707, S.708, N.1071 1 PLIP interactions: 1 interactions with chain I Hydrogen bonds: I:N.1071 NAG-NAG.19: 3 residues within 4Å: Chain I: N.798, S.800, F.814 1 PLIP interactions: 1 interactions with chain I Hydrophobic interactions: I:F.814

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 G: N.1095, H.1098, F.1100 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.13: 4 residues within 4Å: Chain H: N.1095, T.1097, H.1098, F.1100 1 PLIP interactions: 1 interactions with chain H Hydrogen bonds: H:H.1098 NAG-NAG-BMA.14: 1 residues within 4Å: Chain H: N.1131 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.20: 4 residues within 4Å: Chain I: N.1095, T.1097, H.1098, F.1100 1 PLIP interactions: 1 interactions with chain I Hydrogen bonds: I:H.1098 NAG-NAG-BMA.21: 1 residues within 4Å: Chain I: N.1131 No protein-ligand interaction detected (PLIP)

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

NAG.22: 4 residues within 4Å: Chain A: S.76, T.77 Chain G: D.336 Ligands: NAG.26 Ligand excluded by PLIP NAG.23: 2 residues within 4Å: Chain G: Y.1152, N.1155 Ligand excluded by PLIP NAG.24: 2 residues within 4Å: Chain G: N.143, S.251 Ligand excluded by PLIP NAG.25: 2 residues within 4Å: Chain G: C.15, N.17 Ligand excluded by PLIP NAG.26: 3 residues within 4Å: Chain G: N.340, L.368 Ligands: NAG.22 Ligand excluded by PLIP NAG.27: 3 residues within 4Å: Chain G: Y.28, N.30, N.61 Ligand excluded by PLIP NAG.28: 1 residues within 4Å: Chain G: N.600 Ligand excluded by PLIP NAG.29: 1 residues within 4Å: Chain G: N.654 Ligand excluded by PLIP NAG.30: 3 residues within 4Å: Chain G: N.613, C.614, Q.641 Ligand excluded by PLIP NAG.31: 1 residues within 4Å: Chain G: N.706 Ligand excluded by PLIP NAG.32: 8 residues within 4Å: Chain G: D.193, G.194, G.229, I.230 Chain H: K.459, P.460, F.461, E.462 Ligand excluded by PLIP NAG.33: 2 residues within 4Å: Chain H: Y.1152, N.1155 Ligand excluded by PLIP NAG.34: 5 residues within 4Å: Chain H: N.120, A.121, T.122, N.123, E.149 Ligand excluded by PLIP NAG.35: 4 residues within 4Å: Chain H: K.142, N.143, N.144, S.251 Ligand excluded by PLIP NAG.36: 5 residues within 4Å: Chain H: C.15, V.16, N.17, C.134, N.135 Ligand excluded by PLIP NAG.37: 3 residues within 4Å: Chain C: T.77 Chain H: D.336, N.340 Ligand excluded by PLIP NAG.38: 2 residues within 4Å: Chain H: Y.28, N.61 Ligand excluded by PLIP NAG.39: 1 residues within 4Å: Chain H: N.600 Ligand excluded by PLIP NAG.40: 1 residues within 4Å: Chain H: N.654 Ligand excluded by PLIP NAG.41: 2 residues within 4Å: Chain H: N.613, Q.641 Ligand excluded by PLIP NAG.42: 1 residues within 4Å: Chain H: N.706 Ligand excluded by PLIP NAG.43: 2 residues within 4Å: Chain I: Y.1152, N.1155 Ligand excluded by PLIP NAG.44: 4 residues within 4Å: Chain I: N.120, A.121, T.122, N.123 Ligand excluded by PLIP NAG.45: 3 residues within 4Å: Chain I: K.142, N.143, S.251 Ligand excluded by PLIP NAG.46: 3 residues within 4Å: Chain I: C.15, V.16, N.17 Ligand excluded by PLIP NAG.47: 3 residues within 4Å: Chain B: D.74, T.77 Chain I: D.336 Ligand excluded by PLIP NAG.48: 2 residues within 4Å: Chain I: Y.28, N.61 Ligand excluded by PLIP NAG.49: 2 residues within 4Å: Chain I: N.600, T.601 Ligand excluded by PLIP NAG.50: 1 residues within 4Å: Chain I: N.654 Ligand excluded by PLIP NAG.51: 3 residues within 4Å: Chain I: N.613, C.614, Q.641 Ligand excluded by PLIP NAG.52: 1 residues within 4Å: Chain I: 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: ABC
The light chain of Fab XGv347: DEF
Spike glycoprotein: GHI

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
G

B
H

C
I

D
J

E
K

F
L

G
A

H
B

I
C

The heavy chain of Fab XGv347

The light chain of Fab XGv347

Spike glycoprotein

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