SMTL ID : 7wwl.1

S protein of Delta variant in complex with ZWD12

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-mer

Ligands

23 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.1: 3 residues within 4Å: Chain A: N.329, P.577, Q.578 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 4 residues within 4Å: Chain A: F.340, N.341 Chain H: D.102, W.103 1 PLIP interactions: 1 interactions with chain H Hydrophobic interactions: H:D.102 NAG-NAG.3: 4 residues within 4Å: Chain A: N.715, L.920, Q.924, Q.1069 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.920 NAG-NAG.4: 3 residues within 4Å: Chain A: N.799, S.801, Q.802 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 3 residues within 4Å: Chain A: A.704, E.1070, N.1072 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 3 residues within 4Å: Chain A: N.1096, T.1098, F.1101 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 1 residues within 4Å: Chain A: N.1132 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 3 residues within 4Å: Chain B: N.329, Q.578, L.580 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 4 residues within 4Å: Chain B: F.340, N.341 Chain F: D.102, W.103 1 PLIP interactions: 1 interactions with chain F Hydrophobic interactions: F:D.102 NAG-NAG.10: 3 residues within 4Å: Chain B: N.707, G.1129 Chain C: D.794 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 3 residues within 4Å: Chain B: N.715, L.920, Q.924 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:L.920 NAG-NAG.12: 3 residues within 4Å: Chain B: N.799, S.801, Q.802 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 4 residues within 4Å: Chain B: N.1096, T.1098, H.1099, F.1101 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 1 residues within 4Å: Chain B: N.1132 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 3 residues within 4Å: Chain C: N.329, Q.578, L.580 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 4 residues within 4Å: Chain C: F.340, N.341 Chain D: D.102, W.103 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:D.102 NAG-NAG.17: 2 residues within 4Å: Chain A: D.794 Chain C: N.707 No protein-ligand interaction detected (PLIP) NAG-NAG.18: 5 residues within 4Å: Chain C: N.715, L.920, N.923, Q.924, Q.1069 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:L.920, C:N.923 NAG-NAG.19: 2 residues within 4Å: Chain C: N.799, S.801 No protein-ligand interaction detected (PLIP) NAG-NAG.20: 3 residues within 4Å: Chain C: A.704, E.1070, N.1072 No protein-ligand interaction detected (PLIP) NAG-NAG.21: 4 residues within 4Å: Chain C: N.1096, T.1098, H.1099, F.1101 No protein-ligand interaction detected (PLIP) NAG-NAG.22: 1 residues within 4Å: Chain C: N.1132 No protein-ligand interaction detected (PLIP) NAG-NAG.23: 4 residues within 4Å: Chain B: A.704, E.1070, K.1071, N.1072 No protein-ligand interaction detected (PLIP)

25 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.24: 2 residues within 4Å: Chain A: Y.28, N.61 Ligand excluded by PLIP NAG.25: 3 residues within 4Å: Chain A: N.122, T.124, V.127 Ligand excluded by PLIP NAG.26: 2 residues within 4Å: Chain A: E.132, N.163 Ligand excluded by PLIP NAG.27: 3 residues within 4Å: Chain A: G.230, N.232 Chain C: R.464 Ligand excluded by PLIP NAG.28: 4 residues within 4Å: Chain A: N.278, E.279, N.280 Chain C: K.556 Ligand excluded by PLIP NAG.29: 2 residues within 4Å: Chain A: N.601, T.602 Ligand excluded by PLIP NAG.30: 1 residues within 4Å: Chain A: N.614 Ligand excluded by PLIP NAG.31: 1 residues within 4Å: Chain A: N.655 Ligand excluded by PLIP NAG.32: 3 residues within 4Å: Chain A: N.707, G.1129 Chain B: D.794 Ligand excluded by PLIP NAG.33: 2 residues within 4Å: Chain B: Y.28, N.61 Ligand excluded by PLIP NAG.34: 3 residues within 4Å: Chain B: N.122, T.124, V.127 Ligand excluded by PLIP NAG.35: 2 residues within 4Å: Chain B: E.132, N.163 Ligand excluded by PLIP NAG.36: 3 residues within 4Å: Chain A: R.464 Chain B: G.230, N.232 Ligand excluded by PLIP NAG.37: 4 residues within 4Å: Chain A: K.556 Chain B: N.278, E.279, N.280 Ligand excluded by PLIP NAG.38: 2 residues within 4Å: Chain B: N.601, T.602 Ligand excluded by PLIP NAG.39: 1 residues within 4Å: Chain B: N.614 Ligand excluded by PLIP NAG.40: 1 residues within 4Å: Chain B: N.655 Ligand excluded by PLIP NAG.41: 2 residues within 4Å: Chain C: Y.28, N.61 Ligand excluded by PLIP NAG.42: 3 residues within 4Å: Chain C: N.122, T.124, V.127 Ligand excluded by PLIP NAG.43: 2 residues within 4Å: Chain C: E.132, N.163 Ligand excluded by PLIP NAG.44: 3 residues within 4Å: Chain B: R.464 Chain C: G.230, N.232 Ligand excluded by PLIP NAG.45: 4 residues within 4Å: Chain B: K.556 Chain C: N.278, E.279, N.280 Ligand excluded by PLIP NAG.46: 2 residues within 4Å: Chain C: N.601, T.602 Ligand excluded by PLIP NAG.47: 1 residues within 4Å: Chain C: N.614 Ligand excluded by PLIP NAG.48: 1 residues within 4Å: Chain C: N.655 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chi, X. et al., Broadly neutralizing antibodies against Omicron-included SARS-CoV-2 variants induced by vaccination. Signal Transduct Target Ther (2022)

Release Date

2022-06-01

Peptides

Spike glycoprotein: ABC
heavy chain of ZWD12: DFH
light chain of ZWD12: EGI

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
H

F
I

H
J

E
L

G
M

I
N

Spike glycoprotein

heavy chain of ZWD12

light chain of ZWD12

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