SMTL ID : 7we7.1

SARS-CoV-2 Omicron variant spike protein in complex with Fab XGv282

Coordinates

PDB Format Compare

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: 4 residues within 4Å: Chain C: T.106, N.231, T.233 Chain D: K.459 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 2 residues within 4Å: Chain C: N.328, Q.577 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 4 residues within 4Å: Chain C: N.714, L.919, Q.923, Q.1068 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 2 residues within 4Å: Chain C: A.703, N.1071 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:A.703 NAG-NAG.5: 3 residues within 4Å: Chain C: N.798, S.800, Q.801 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 1 residues within 4Å: Chain C: N.1131 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 1 residues within 4Å: Chain D: I.230 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 3 residues within 4Å: Chain D: N.328, I.329, Q.577 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:Q.577 NAG-NAG.10: 4 residues within 4Å: Chain D: N.714, L.919, Q.923, Q.1068 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 6 residues within 4Å: Chain C: Q.892 Chain D: A.703, S.705, N.707, S.708, N.1071 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:N.1071, C:Q.892 NAG-NAG.12: 2 residues within 4Å: Chain D: N.798, S.800 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 8 residues within 4Å: Chain C: R.451, E.462, R.463, D.464, I.465, S.466 Chain E: N.231, T.233 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:D.464, C:I.465 Hydrogen bonds: C:D.464 NAG-NAG.16: 4 residues within 4Å: Chain E: N.328, I.329, T.330, Q.577 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:N.328, E:N.328 NAG-NAG.17: 3 residues within 4Å: Chain E: N.714, L.919, Q.923 No protein-ligand interaction detected (PLIP) NAG-NAG.18: 4 residues within 4Å: Chain E: S.705, N.707, S.708, N.1071 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:N.1071 NAG-NAG.19: 4 residues within 4Å: Chain E: N.798, S.800, Q.801, F.814 1 PLIP interactions: 1 interactions with chain E Hydrophobic interactions: E: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: 4 residues within 4Å: Chain C: N.1095, T.1097, H.1098, F.1100 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.13: 4 residues within 4Å: Chain D: N.1095, T.1097, H.1098, F.1100 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.14: 1 residues within 4Å: Chain D: N.1131 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.20: 4 residues within 4Å: Chain E: N.1095, T.1097, H.1098, F.1100 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.21: 1 residues within 4Å: Chain E: N.1131 No protein-ligand interaction detected (PLIP)

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

NAG.22: 9 residues within 4Å: Chain C: D.193, G.194, G.229, I.230, N.231, I.232 Chain D: K.459, F.461, E.462 Ligand excluded by PLIP NAG.23: 2 residues within 4Å: Chain C: Y.1152, N.1155 Ligand excluded by PLIP NAG.24: 2 residues within 4Å: Chain C: N.143, S.251 Ligand excluded by PLIP NAG.25: 3 residues within 4Å: Chain C: C.15, N.17, N.135 Ligand excluded by PLIP NAG.26: 2 residues within 4Å: Chain C: Y.28, N.61 Ligand excluded by PLIP NAG.27: 1 residues within 4Å: Chain C: N.600 Ligand excluded by PLIP NAG.28: 1 residues within 4Å: Chain C: N.654 Ligand excluded by PLIP NAG.29: 2 residues within 4Å: Chain C: N.613, Q.641 Ligand excluded by PLIP NAG.30: 2 residues within 4Å: Chain C: N.706 Chain E: Y.793 Ligand excluded by PLIP NAG.31: 3 residues within 4Å: Chain D: Y.1152, N.1155 Chain E: T.1157 Ligand excluded by PLIP NAG.32: 4 residues within 4Å: Chain D: N.120, A.121, N.123, E.149 Ligand excluded by PLIP NAG.33: 4 residues within 4Å: Chain D: K.142, N.143, N.144, S.251 Ligand excluded by PLIP NAG.34: 5 residues within 4Å: Chain D: C.15, V.16, N.17, C.134, N.135 Ligand excluded by PLIP NAG.35: 3 residues within 4Å: Chain D: Y.28, N.30, N.61 Ligand excluded by PLIP NAG.36: 2 residues within 4Å: Chain D: N.600, T.601 Ligand excluded by PLIP NAG.37: 1 residues within 4Å: Chain D: N.654 Ligand excluded by PLIP NAG.38: 2 residues within 4Å: Chain D: N.613, Q.641 Ligand excluded by PLIP NAG.39: 2 residues within 4Å: Chain C: Y.793 Chain D: N.706 Ligand excluded by PLIP NAG.40: 2 residues within 4Å: Chain E: K.1151, N.1155 Ligand excluded by PLIP NAG.41: 4 residues within 4Å: Chain E: N.120, A.121, T.122, N.123 Ligand excluded by PLIP NAG.42: 3 residues within 4Å: Chain E: K.142, N.143, S.251 Ligand excluded by PLIP NAG.43: 3 residues within 4Å: Chain E: C.15, V.16, N.17 Ligand excluded by PLIP NAG.44: 2 residues within 4Å: Chain E: Y.28, N.61 Ligand excluded by PLIP NAG.45: 2 residues within 4Å: Chain E: N.600, T.601 Ligand excluded by PLIP NAG.46: 1 residues within 4Å: Chain E: N.654 Ligand excluded by PLIP NAG.47: 3 residues within 4Å: Chain E: N.613, C.614, Q.641 Ligand excluded by PLIP NAG.48: 2 residues within 4Å: Chain D: Y.793 Chain E: 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

Heavy chain of Fab 282: AFH
The light chain of Fab 282: BGI
Spike glycoprotein: CDE

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
H

F
J

H
K

B
L

G
M

I
N

C
D

D
E

E
G

Heavy chain of Fab 282

The light chain of Fab 282

Spike glycoprotein

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