SMTL ID : 8g76.1

SARS-CoV-2 spike/Nb5 complex

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-mer

Ligands

10 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.704, T.706, Q.913 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 3 residues within 4Å: Chain A: N.788, S.790, Q.791 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 4 residues within 4Å: Chain A: N.1085, T.1087, H.1088, F.1090 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 3 residues within 4Å: Chain B: N.788, S.790, Q.791 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 4 residues within 4Å: Chain B: N.1085, T.1087, H.1088, F.1090 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 2 residues within 4Å: Chain B: I.1119, N.1121 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 2 residues within 4Å: Chain C: N.704, Q.913 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 3 residues within 4Å: Chain C: N.788, S.790, Q.791 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 4 residues within 4Å: Chain C: N.1085, T.1087, H.1088, F.1090 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 2 residues within 4Å: Chain C: I.1119, N.1121 No protein-ligand interaction detected (PLIP)

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

NAG.11: 1 residues within 4Å: Chain A: N.1121 Ligand excluded by PLIP NAG.12: 3 residues within 4Å: Chain A: N.318, T.320, Q.567 Ligand excluded by PLIP NAG.13: 3 residues within 4Å: Chain A: G.326, F.329, N.330 Ligand excluded by PLIP NAG.14: 2 residues within 4Å: Chain A: N.603, R.633 Ligand excluded by PLIP NAG.15: 2 residues within 4Å: Chain A: H.642, N.644 Ligand excluded by PLIP NAG.16: 2 residues within 4Å: Chain A: N.696, G.1118 Ligand excluded by PLIP NAG.17: 2 residues within 4Å: Chain A: A.693, N.1061 Ligand excluded by PLIP NAG.18: 5 residues within 4Å: Chain A: Y.15, N.48 Chain D: N.75, A.76, N.78 Ligand excluded by PLIP NAG.19: 2 residues within 4Å: Chain A: N.151, N.152 Ligand excluded by PLIP NAG.20: 1 residues within 4Å: Chain A: N.590 Ligand excluded by PLIP NAG.21: 3 residues within 4Å: Chain A: T.95, N.221, T.223 Ligand excluded by PLIP NAG.22: 3 residues within 4Å: Chain B: T.95, N.221, T.223 Ligand excluded by PLIP NAG.23: 2 residues within 4Å: Chain B: N.318, Q.567 Ligand excluded by PLIP NAG.24: 3 residues within 4Å: Chain B: G.588, N.590, T.591 Ligand excluded by PLIP NAG.25: 3 residues within 4Å: Chain B: N.603, T.605, E.606 Ligand excluded by PLIP NAG.26: 2 residues within 4Å: Chain B: H.642, N.644 Ligand excluded by PLIP NAG.27: 2 residues within 4Å: Chain B: N.696, G.1118 Ligand excluded by PLIP NAG.28: 1 residues within 4Å: Chain B: N.704 Ligand excluded by PLIP NAG.29: 1 residues within 4Å: Chain B: N.1061 Ligand excluded by PLIP NAG.30: 5 residues within 4Å: Chain B: Y.15, N.48 Chain E: F.31, N.75, A.76 Ligand excluded by PLIP NAG.31: 3 residues within 4Å: Chain B: E.119, N.151, N.152 Ligand excluded by PLIP NAG.32: 2 residues within 4Å: Chain B: E.268, N.269 Ligand excluded by PLIP NAG.33: 6 residues within 4Å: Chain C: Y.15, N.48 Chain F: F.31, N.75, A.76, N.78 Ligand excluded by PLIP NAG.34: 2 residues within 4Å: Chain C: E.268, N.269 Ligand excluded by PLIP NAG.35: 2 residues within 4Å: Chain C: N.318, T.320 Ligand excluded by PLIP NAG.36: 3 residues within 4Å: Chain C: N.603, T.605, E.606 Ligand excluded by PLIP NAG.37: 3 residues within 4Å: Chain C: H.642, V.643, N.644 Ligand excluded by PLIP NAG.38: 3 residues within 4Å: Chain A: D.783 Chain C: N.696, G.1118 Ligand excluded by PLIP NAG.39: 2 residues within 4Å: Chain C: A.693, N.1061 Ligand excluded by PLIP NAG.40: 2 residues within 4Å: Chain C: N.4, N.124 Ligand excluded by PLIP NAG.41: 2 residues within 4Å: Chain C: N.151, N.152 Ligand excluded by PLIP NAG.42: 1 residues within 4Å: Chain C: N.330 Ligand excluded by PLIP NAG.43: 1 residues within 4Å: Chain C: N.590 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ye, G. et al., Dual-role epitope on SARS-CoV-2 spike enhances and neutralizes viral entry across different variants. Plos Pathog. (2024)

Release Date

2024-02-21

Peptides

Spike glycoprotein: ABC
Nanosota-5: DEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
D

D
E

E
H

F
I

Spike glycoprotein

Nanosota-5

Related Entries With Identical Sequence