SMTL ID : 7we9.1

SARS-CoV-2 Omicron variant spike protein in complex with Fab XGv289

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)(Non-functional Binders)

NAG-NAG.1: 6 residues within 4Å: Chain A: T.106, N.231 Chain B: R.454, N.457, K.459 Ligands: NAG.21 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 2 residues within 4Å: Chain A: N.328, Q.577 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: 2 residues within 4Å: Chain A: N.1071, F.1072 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: 2 residues within 4Å: Chain A: I.1129, N.1131 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 1 residues within 4Å: Chain B: N.231 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.231 NAG-NAG.9: 2 residues within 4Å: Chain B: N.328, Q.577 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 2 residues within 4Å: Chain B: N.714, L.919 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) NAG-NAG.12: 3 residues within 4Å: Chain B: N.798, S.800, Q.801 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 1 residues within 4Å: Chain C: N.231 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 1 residues within 4Å: Chain C: N.714 No protein-ligand interaction detected (PLIP) NAG-NAG.17: 1 residues within 4Å: Chain C: N.1071 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.1071 NAG-NAG.18: 1 residues within 4Å: Chain C: N.798 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: 2 residues within 4Å: Chain A: N.1095, T.1097 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.1097 NAG-NAG-BMA.13: 4 residues within 4Å: Chain B: N.1095, T.1097, H.1098, F.1100 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.14: 2 residues within 4Å: Chain B: I.1129, N.1131 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.19: 3 residues within 4Å: Chain C: N.1095, T.1097, H.1098 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.20: 3 residues within 4Å: Chain C: C.1079, C.1123, N.1131 No protein-ligand interaction detected (PLIP)

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

NAG.21: 6 residues within 4Å: Chain A: D.86, N.191, N.231, I.232 Chain B: K.459 Ligands: NAG-NAG.1 Ligand excluded by PLIP NAG.22: 2 residues within 4Å: Chain A: K.1151, N.1155 Ligand excluded by PLIP NAG.23: 5 residues within 4Å: Chain A: L.139, D.140, K.142, N.143, W.255 Ligand excluded by PLIP NAG.24: 3 residues within 4Å: Chain A: N.17, L.18, T.19 Ligand excluded by PLIP NAG.25: 2 residues within 4Å: Chain A: Y.28, N.61 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, T.615 Ligand excluded by PLIP NAG.29: 2 residues within 4Å: Chain A: N.706, N.707 Ligand excluded by PLIP NAG.30: 1 residues within 4Å: Chain B: N.1155 Ligand excluded by PLIP NAG.31: 2 residues within 4Å: Chain B: N.120, N.123 Ligand excluded by PLIP NAG.32: 2 residues within 4Å: Chain B: K.142, N.143 Ligand excluded by PLIP NAG.33: 2 residues within 4Å: Chain B: C.15, N.17 Ligand excluded by PLIP NAG.34: 2 residues within 4Å: Chain B: Y.28, 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: 1 residues within 4Å: Chain B: N.654 Ligand excluded by PLIP NAG.37: 1 residues within 4Å: Chain B: N.613 Ligand excluded by PLIP NAG.38: 1 residues within 4Å: Chain B: N.706 Ligand excluded by PLIP NAG.39: 1 residues within 4Å: Chain C: N.1155 Ligand excluded by PLIP NAG.40: 3 residues within 4Å: Chain C: A.121, T.122, N.123 Ligand excluded by PLIP NAG.41: 2 residues within 4Å: Chain C: K.142, N.143 Ligand excluded by PLIP NAG.42: 4 residues within 4Å: Chain C: N.17, V.81, N.135, D.136 Ligand excluded by PLIP NAG.43: 2 residues within 4Å: Chain C: Y.28, N.61 Ligand excluded by PLIP NAG.44: 2 residues within 4Å: Chain C: E.306, N.600 Ligand excluded by PLIP NAG.45: 1 residues within 4Å: Chain C: N.654 Ligand excluded by PLIP NAG.46: 2 residues within 4Å: Chain C: N.613, Q.641 Ligand excluded by PLIP NAG.47: 2 residues within 4Å: Chain B: I.791 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 XGv289: DEF
The light chain of Fab XGv289: GHI

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
F

D
C

E
H

F
I

G
J

H
K

I
L

Spike glycoprotein

The heavy chain of Fab XGv289

The light chain of Fab XGv289

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