SMTL ID : 8hld.1

S protein of SARS-CoV-2 in complex with 26434

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-mer

Ligands

31 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.122, T.124, S.151 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 2 residues within 4Å: Chain A: N.164, N.165 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 2 residues within 4Å: Chain A: T.108, N.234 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 3 residues within 4Å: Chain A: N.331, Q.580, L.582 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 2 residues within 4Å: Chain A: F.342, N.343 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 4 residues within 4Å: Chain A: N.717, L.922, Q.926, Q.1071 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.922 NAG-NAG.7: 3 residues within 4Å: Chain A: N.801, S.803, Q.804 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 3 residues within 4Å: Chain A: A.706, E.1072, N.1074 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 3 residues within 4Å: Chain A: N.1098, T.1100, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 1 residues within 4Å: Chain A: N.1134 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 3 residues within 4Å: Chain B: N.122, T.124, S.151 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 2 residues within 4Å: Chain B: N.164, N.165 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 2 residues within 4Å: Chain B: T.108, N.234 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 3 residues within 4Å: Chain B: N.331, P.579, Q.580 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 2 residues within 4Å: Chain B: F.342, N.343 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 3 residues within 4Å: Chain B: N.709, G.1131 Chain C: D.796 No protein-ligand interaction detected (PLIP) NAG-NAG.17: 3 residues within 4Å: Chain B: N.717, L.922, Q.926 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:L.922 NAG-NAG.18: 3 residues within 4Å: Chain B: N.801, S.803, Q.804 No protein-ligand interaction detected (PLIP) NAG-NAG.19: 4 residues within 4Å: Chain B: N.1098, T.1100, H.1101, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG.20: 1 residues within 4Å: Chain B: N.1134 No protein-ligand interaction detected (PLIP) NAG-NAG.21: 3 residues within 4Å: Chain C: N.122, T.124, S.151 No protein-ligand interaction detected (PLIP) NAG-NAG.22: 2 residues within 4Å: Chain C: N.164, N.165 No protein-ligand interaction detected (PLIP) NAG-NAG.23: 2 residues within 4Å: Chain C: T.108, N.234 No protein-ligand interaction detected (PLIP) NAG-NAG.24: 2 residues within 4Å: Chain C: N.331, Q.580 No protein-ligand interaction detected (PLIP) NAG-NAG.25: 2 residues within 4Å: Chain C: F.342, N.343 No protein-ligand interaction detected (PLIP) NAG-NAG.26: 2 residues within 4Å: Chain A: D.796 Chain C: N.709 No protein-ligand interaction detected (PLIP) NAG-NAG.27: 5 residues within 4Å: Chain C: N.717, L.922, N.925, Q.926, Q.1071 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:L.922, C:N.925 NAG-NAG.28: 2 residues within 4Å: Chain C: N.801, S.803 No protein-ligand interaction detected (PLIP) NAG-NAG.29: 3 residues within 4Å: Chain C: A.706, E.1072, N.1074 No protein-ligand interaction detected (PLIP) NAG-NAG.30: 4 residues within 4Å: Chain C: N.1098, T.1100, H.1101, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG.31: 1 residues within 4Å: Chain C: N.1134 No protein-ligand interaction detected (PLIP)

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

NAG.32: 1 residues within 4Å: Chain A: N.17 Ligand excluded by PLIP NAG.33: 2 residues within 4Å: Chain A: Y.28, N.61 Ligand excluded by PLIP NAG.34: 2 residues within 4Å: Chain A: K.147, N.149 Ligand excluded by PLIP NAG.35: 4 residues within 4Å: Chain A: N.280, E.281, N.282 Chain C: K.558 Ligand excluded by PLIP NAG.36: 2 residues within 4Å: Chain A: N.603, T.604 Ligand excluded by PLIP NAG.37: 1 residues within 4Å: Chain A: N.616 Ligand excluded by PLIP NAG.38: 1 residues within 4Å: Chain A: N.657 Ligand excluded by PLIP NAG.39: 3 residues within 4Å: Chain A: N.709, G.1131 Chain B: D.796 Ligand excluded by PLIP NAG.40: 1 residues within 4Å: Chain B: N.17 Ligand excluded by PLIP NAG.41: 2 residues within 4Å: Chain B: Y.28, N.61 Ligand excluded by PLIP NAG.42: 2 residues within 4Å: Chain B: K.147, N.149 Ligand excluded by PLIP NAG.43: 3 residues within 4Å: Chain B: N.280, E.281, N.282 Ligand excluded by PLIP NAG.44: 2 residues within 4Å: Chain B: N.603, T.604 Ligand excluded by PLIP NAG.45: 1 residues within 4Å: Chain B: N.616 Ligand excluded by PLIP NAG.46: 1 residues within 4Å: Chain B: N.657 Ligand excluded by PLIP NAG.47: 5 residues within 4Å: Chain B: A.706, E.1072, K.1073, N.1074 Ligands: NAG.48 Ligand excluded by PLIP NAG.48: 1 residues within 4Å: Ligands: NAG.47 Ligand excluded by PLIP NAG.49: 1 residues within 4Å: Chain C: N.17 Ligand excluded by PLIP NAG.50: 2 residues within 4Å: Chain C: Y.28, N.61 Ligand excluded by PLIP NAG.51: 2 residues within 4Å: Chain C: K.147, N.149 Ligand excluded by PLIP NAG.52: 4 residues within 4Å: Chain B: K.558 Chain C: N.280, E.281, N.282 Ligand excluded by PLIP NAG.53: 2 residues within 4Å: Chain C: N.603, T.604 Ligand excluded by PLIP NAG.54: 1 residues within 4Å: Chain C: N.616 Ligand excluded by PLIP NAG.55: 1 residues within 4Å: Chain C: N.657 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhang, Y.Y. et al., A SARS-CoV-2 Spike N-terminal domain neutralizing antibody targets on a glycans shielded silent face and inhibits virus entry via hindering the recognition of RBD and hACE2. To Be Published

Release Date

2024-06-05

Peptides

Spike glycoprotein: ABC
heavy chain of 26434: DFH
light chain of 26434: 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 26434

light chain of 26434

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