SMTL ID : 7xic.1

S-ECD (Omicron) in complex with STS165

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-mer

Ligands

19 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: 4 residues within 4Å: Chain A: N.328, I.329, P.576, Q.577 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 3 residues within 4Å: Chain A: N.714, L.919, Q.1068 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 1 residues within 4Å: Chain A: N.798 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 4 residues within 4Å: Chain A: S.701, A.703, E.1069, N.1071 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:A.703 NAG-NAG.5: 3 residues within 4Å: Chain A: N.1095, T.1097, H.1098 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 1 residues within 4Å: Chain A: N.1131 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 2 residues within 4Å: Chain B: N.328, Q.577 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 1 residues within 4Å: Chain B: N.706 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 3 residues within 4Å: Chain B: N.714, L.919, Q.923 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:L.919 NAG-NAG.10: 3 residues within 4Å: Chain B: N.798, S.800, Q.801 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 3 residues within 4Å: Chain B: N.1095, T.1097, H.1098 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 1 residues within 4Å: Chain B: N.1131 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 2 residues within 4Å: Chain C: N.328, Q.577 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 2 residues within 4Å: Chain C: N.706, I.1127 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 4 residues within 4Å: Chain C: N.714, L.919, Q.923, Q.1068 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:L.919, C:Q.923 NAG-NAG.16: 3 residues within 4Å: Chain C: N.798, S.800, Q.801 No protein-ligand interaction detected (PLIP) NAG-NAG.17: 3 residues within 4Å: Chain C: A.703, E.1069, N.1071 No protein-ligand interaction detected (PLIP) NAG-NAG.18: 3 residues within 4Å: Chain C: N.1095, T.1097, H.1098 No protein-ligand interaction detected (PLIP) NAG-NAG.19: 1 residues within 4Å: Chain C: N.1131 No protein-ligand interaction detected (PLIP)

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

NAG.20: 3 residues within 4Å: Chain A: Y.28, N.30, N.61 Ligand excluded by PLIP NAG.21: 4 residues within 4Å: Chain A: N.120, T.122, V.125, F.152 Ligand excluded by PLIP NAG.22: 1 residues within 4Å: Chain A: N.160 Ligand excluded by PLIP NAG.23: 2 residues within 4Å: Chain A: G.229, N.231 Ligand excluded by PLIP NAG.24: 2 residues within 4Å: Chain A: N.279 Chain C: K.555 Ligand excluded by PLIP NAG.25: 3 residues within 4Å: Chain A: D.336, N.340 Ligands: NAG.26 Ligand excluded by PLIP NAG.26: 1 residues within 4Å: Ligands: NAG.25 Ligand excluded by PLIP NAG.27: 1 residues within 4Å: Chain A: N.600 Ligand excluded by PLIP NAG.28: 3 residues within 4Å: Chain A: N.613, T.615, Q.641 Ligand excluded by PLIP NAG.29: 2 residues within 4Å: Chain A: Y.652, N.654 Ligand excluded by PLIP NAG.30: 3 residues within 4Å: Chain A: N.706, I.1127, G.1128 Ligand excluded by PLIP NAG.31: 3 residues within 4Å: Chain B: Y.28, N.30, N.61 Ligand excluded by PLIP NAG.32: 2 residues within 4Å: Chain B: N.120, T.122 Ligand excluded by PLIP NAG.33: 1 residues within 4Å: Chain B: N.160 Ligand excluded by PLIP NAG.34: 2 residues within 4Å: Chain B: G.229, N.231 Ligand excluded by PLIP NAG.35: 1 residues within 4Å: Chain B: N.279 Ligand excluded by PLIP NAG.36: 3 residues within 4Å: Chain B: D.336, N.340 Ligands: NAG.37 Ligand excluded by PLIP NAG.37: 1 residues within 4Å: Ligands: NAG.36 Ligand excluded by PLIP NAG.38: 1 residues within 4Å: Chain B: N.600 Ligand excluded by PLIP NAG.39: 3 residues within 4Å: Chain B: N.613, T.615, Q.641 Ligand excluded by PLIP NAG.40: 2 residues within 4Å: Chain B: Y.652, N.654 Ligand excluded by PLIP NAG.41: 4 residues within 4Å: Chain B: A.703, E.1069, N.1071 Ligands: NAG.42 Ligand excluded by PLIP NAG.42: 1 residues within 4Å: Ligands: NAG.41 Ligand excluded by PLIP NAG.43: 3 residues within 4Å: Chain C: Y.28, N.30, N.61 Ligand excluded by PLIP NAG.44: 3 residues within 4Å: Chain C: N.120, T.122, V.125 Ligand excluded by PLIP NAG.45: 1 residues within 4Å: Chain C: N.160 Ligand excluded by PLIP NAG.46: 2 residues within 4Å: Chain C: G.229, N.231 Ligand excluded by PLIP NAG.47: 1 residues within 4Å: Chain C: N.279 Ligand excluded by PLIP NAG.48: 3 residues within 4Å: Chain C: D.336, N.340 Ligands: NAG.49 Ligand excluded by PLIP NAG.49: 1 residues within 4Å: Ligands: NAG.48 Ligand excluded by PLIP NAG.50: 1 residues within 4Å: Chain C: N.600 Ligand excluded by PLIP NAG.51: 2 residues within 4Å: Chain C: N.613, Q.641 Ligand excluded by PLIP NAG.52: 2 residues within 4Å: Chain C: Y.652, N.654 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Li, Y. et al., Structural and functional analysis of an inter-Spike bivalent neutralizing antibody against SARS-CoV-2 variants. Iscience (2022)

Release Date

2022-06-15

Peptides

Spike glycoprotein: ABC
heavy chain of STS165: DFH
light chain of STS165: EGI

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
E

F
H

H
K

E
F

G
I

I
L

Spike glycoprotein

heavy chain of STS165

light chain of STS165

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