SMTL ID : 7wtk.1

SARS-CoV-2 Omicron variant spike in complex with Fab XGv286

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-mer

Ligands

12 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: 2 residues within 4Å: Chain A: N.701, Q.910 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 2 residues within 4Å: Chain A: N.1058, F.1059 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.1058 NAG-NAG.3: 1 residues within 4Å: Chain A: N.785 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) NAG-NAG.7: 4 residues within 4Å: Chain D: N.315, I.316, Q.564, T.565 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:T.565 Hydrogen bonds: D:N.315 NAG-NAG.8: 1 residues within 4Å: Chain D: N.701 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) NAG-NAG.10: 3 residues within 4Å: Chain D: N.785, S.787, Q.788 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 1 residues within 4Å: Chain E: N.218 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 2 residues within 4Å: Chain E: N.701, Q.910 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 1 residues within 4Å: Chain E: N.1058 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:N.1058 NAG-NAG.16: 3 residues within 4Å: Chain E: N.785, S.787, Q.788 No protein-ligand interaction detected (PLIP)

6 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.4: 3 residues within 4Å: Chain A: N.1082, H.1085, F.1087 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.5: 3 residues within 4Å: Chain A: C.1066, C.1110, N.1118 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.11: 3 residues within 4Å: Chain D: N.1082, T.1084, H.1085 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.12: 2 residues within 4Å: Chain D: I.1116, N.1118 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.17: 4 residues within 4Å: Chain E: N.1082, T.1084, H.1085, F.1087 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.18: 3 residues within 4Å: Chain E: C.1066, C.1110, N.1118 No protein-ligand interaction detected (PLIP)

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

NAG.19: 2 residues within 4Å: Chain A: Y.1139, N.1142 Ligand excluded by PLIP NAG.20: 1 residues within 4Å: Chain A: T.109 Ligand excluded by PLIP NAG.21: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP NAG.22: 3 residues within 4Å: Chain A: Y.15, N.17, N.48 Ligand excluded by PLIP NAG.23: 7 residues within 4Å: Chain A: N.178, G.181, G.216, I.217, N.218 Chain D: K.446 Ligands: NAG.28 Ligand excluded by PLIP NAG.24: 1 residues within 4Å: Chain A: N.587 Ligand excluded by PLIP NAG.25: 1 residues within 4Å: Chain A: N.641 Ligand excluded by PLIP NAG.26: 2 residues within 4Å: Chain A: N.600, Q.628 Ligand excluded by PLIP NAG.27: 2 residues within 4Å: Chain A: N.693 Chain E: Y.780 Ligand excluded by PLIP NAG.28: 8 residues within 4Å: Chain A: G.216 Chain D: R.438, R.441, F.448, E.449, R.450, D.451 Ligands: NAG.23 Ligand excluded by PLIP NAG.29: 1 residues within 4Å: Chain D: N.1142 Ligand excluded by PLIP NAG.30: 2 residues within 4Å: Chain D: N.107, N.110 Ligand excluded by PLIP NAG.31: 2 residues within 4Å: Chain D: N.130, N.131 Ligand excluded by PLIP NAG.32: 2 residues within 4Å: Chain D: C.2, N.4 Ligand excluded by PLIP NAG.33: 2 residues within 4Å: Chain D: Y.15, N.48 Ligand excluded by PLIP NAG.34: 3 residues within 4Å: Chain D: G.585, N.587, T.588 Ligand excluded by PLIP NAG.35: 1 residues within 4Å: Chain D: N.641 Ligand excluded by PLIP NAG.36: 2 residues within 4Å: Chain D: N.600, T.602 Ligand excluded by PLIP NAG.37: 1 residues within 4Å: Chain D: N.693 Ligand excluded by PLIP NAG.38: 1 residues within 4Å: Chain E: N.1142 Ligand excluded by PLIP NAG.39: 4 residues within 4Å: Chain E: N.107, A.108, T.109, N.110 Ligand excluded by PLIP NAG.40: 3 residues within 4Å: Chain E: K.129, N.130, S.238 Ligand excluded by PLIP NAG.41: 6 residues within 4Å: Chain E: V.3, N.4, R.8, N.66, P.67, D.123 Ligand excluded by PLIP NAG.42: 2 residues within 4Å: Chain E: Y.15, N.48 Ligand excluded by PLIP NAG.43: 1 residues within 4Å: Chain E: N.587 Ligand excluded by PLIP NAG.44: 1 residues within 4Å: Chain E: N.641 Ligand excluded by PLIP NAG.45: 3 residues within 4Å: Chain E: N.600, C.601, Q.628 Ligand excluded by PLIP NAG.46: 2 residues within 4Å: Chain D: Y.780 Chain E: N.693 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, L. et al., Selection and structural bases of potent broadly neutralizing antibodies from 3-dose vaccinees that are highly effective against diverse SARS-CoV-2 variants, including Omicron sublineages. Cell Res. (2022)

Release Date

2022-12-14

Peptides

Spike glycoprotein: ADE
Heavy chain of XGv286: BFG
Light chain of XGv286: CHI

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

D
B

E
A

B
H

F
G

G
I

C
L

H
J

I
K

Spike glycoprotein

Heavy chain of XGv286

Light chain of XGv286

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