SMTL ID : 7wbh.1

overall structure of hu33 and spike

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-2-3-3-mer

Ligands

3 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.1: 4 residues within 4Å: Chain A: F.312, G.313, N.317 Chain D: D.62 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.2: 5 residues within 4Å: Chain B: F.312, G.313, N.317 Chain F: D.62, R.65 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:D.62, F:R.65 NAG-NAG-BMA.3: 5 residues within 4Å: Chain C: F.312, G.313, N.317 Chain H: D.62, R.65 No protein-ligand interaction detected (PLIP)

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

NAG-NAG.4: 1 residues within 4Å: Chain A: N.305 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 3 residues within 4Å: Chain A: N.691, L.896, Q.900 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.896 NAG-NAG.6: 3 residues within 4Å: Chain A: N.775, S.777, Q.778 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 3 residues within 4Å: Chain A: A.680, E.1046, N.1048 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 4 residues within 4Å: Chain A: N.1072, T.1074, H.1075, F.1077 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 2 residues within 4Å: Chain B: N.775, S.777 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 3 residues within 4Å: Chain B: A.680, E.1046, N.1048 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 3 residues within 4Å: Chain C: N.691, L.896, Q.900 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 2 residues within 4Å: Chain C: N.775, S.777 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 3 residues within 4Å: Chain C: A.680, E.1046, N.1048 No protein-ligand interaction detected (PLIP)

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

NAG.14: 1 residues within 4Å: Chain A: N.256 Ligand excluded by PLIP NAG.15: 3 residues within 4Å: Chain A: T.281, T.576, N.577 Ligand excluded by PLIP NAG.16: 1 residues within 4Å: Chain A: N.590 Ligand excluded by PLIP NAG.17: 1 residues within 4Å: Chain A: N.631 Ligand excluded by PLIP NAG.18: 1 residues within 4Å: Chain A: N.683 Ligand excluded by PLIP NAG.19: 1 residues within 4Å: Chain A: N.1108 Ligand excluded by PLIP NAG.20: 1 residues within 4Å: Chain B: N.96 Ligand excluded by PLIP NAG.21: 2 residues within 4Å: Chain A: R.329 Chain B: N.139 Ligand excluded by PLIP NAG.22: 2 residues within 4Å: Chain B: N.254, N.256 Ligand excluded by PLIP NAG.23: 3 residues within 4Å: Chain B: N.305, I.306, Q.554 Ligand excluded by PLIP NAG.24: 1 residues within 4Å: Chain B: N.577 Ligand excluded by PLIP NAG.25: 2 residues within 4Å: Chain B: N.590, T.592 Ligand excluded by PLIP NAG.26: 1 residues within 4Å: Chain B: N.631 Ligand excluded by PLIP NAG.27: 2 residues within 4Å: Chain B: N.683, G.1105 Ligand excluded by PLIP NAG.28: 4 residues within 4Å: Chain B: N.691, L.896, Q.900, Q.1045 Ligand excluded by PLIP NAG.29: 3 residues within 4Å: Chain B: N.1072, T.1074, H.1075 Ligand excluded by PLIP NAG.30: 1 residues within 4Å: Chain B: N.1108 Ligand excluded by PLIP NAG.31: 4 residues within 4Å: Chain B: K.532 Chain C: N.254, N.256, T.258 Ligand excluded by PLIP NAG.32: 2 residues within 4Å: Chain C: N.305, Q.554 Ligand excluded by PLIP NAG.33: 1 residues within 4Å: Chain C: N.577 Ligand excluded by PLIP NAG.34: 1 residues within 4Å: Chain C: N.590 Ligand excluded by PLIP NAG.35: 1 residues within 4Å: Chain C: N.631 Ligand excluded by PLIP NAG.36: 3 residues within 4Å: Chain A: D.770 Chain C: N.683, G.1105 Ligand excluded by PLIP NAG.37: 4 residues within 4Å: Chain C: N.1072, T.1074, H.1075, F.1077 Ligand excluded by PLIP NAG.38: 1 residues within 4Å: Chain C: N.1108 Ligand excluded by PLIP NAG.39: 2 residues within 4Å: Chain A: N.139 Chain I: N.31 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Duan, X. et al., A non-ACE2-blocking neutralizing antibody against Omicron-included SARS-CoV-2 variants. Signal Transduct Target Ther (2022)

Release Date

2022-10-26

Peptides

Spike glycoprotein: A
Spike glycoprotein: BC
heavy chain of hu33: DFH
light chain of hu33: EGI

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
U

F
O

H
P

E
V

G
Q

I
S

Spike glycoprotein

Spike glycoprotein

heavy chain of hu33

light chain of hu33

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