SMTL ID : 8ug9.1

XBB.1.5 spike/Nb5 complex

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-mer

Ligands

12 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG.1: 5 residues within 4Å: Chain A: F.29, N.73, A.74 Chain D: Y.12, N.45 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 7 residues within 4Å: Chain B: I.28, F.29, N.73, A.74, N.76 Chain E: Y.12, N.45 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 6 residues within 4Å: Chain C: F.29, N.73, A.74, N.76 Chain F: Y.12, N.45 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:Y.12, F:Y.12 NAG-NAG.4: 2 residues within 4Å: Chain D: N.700, L.905 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:L.905 NAG-NAG.5: 2 residues within 4Å: Chain D: N.784, S.786 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 4 residues within 4Å: Chain D: N.1081, T.1083, H.1084, F.1086 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 2 residues within 4Å: Chain E: N.700, L.905 1 PLIP interactions: 1 interactions with chain E Hydrophobic interactions: E:L.905 NAG-NAG.8: 2 residues within 4Å: Chain E: N.784, S.786 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 4 residues within 4Å: Chain E: N.1081, T.1083, H.1084, F.1086 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 2 residues within 4Å: Chain F: N.700, L.905 1 PLIP interactions: 1 interactions with chain F Hydrophobic interactions: F:L.905 NAG-NAG.11: 2 residues within 4Å: Chain F: N.784, S.786 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 4 residues within 4Å: Chain F: N.1081, T.1083, H.1084, F.1086 No protein-ligand interaction detected (PLIP)

33 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose

NAG.13: 3 residues within 4Å: Chain D: N.106, T.108, N.109 Ligand excluded by PLIP NAG.14: 2 residues within 4Å: Chain D: N.147, N.148 Ligand excluded by PLIP NAG.15: 9 residues within 4Å: Chain D: T.92, N.217, T.219 Chain F: R.440, K.441, K.443, L.444, K.445, E.448 Ligand excluded by PLIP NAG.16: 4 residues within 4Å: Chain D: N.263, E.264, N.265 Chain F: K.541 Ligand excluded by PLIP NAG.17: 2 residues within 4Å: Chain D: N.314, Q.563 Ligand excluded by PLIP NAG.18: 2 residues within 4Å: Chain D: H.322, N.326 Ligand excluded by PLIP NAG.19: 3 residues within 4Å: Chain D: N.599, T.601 Chain E: I.817 Ligand excluded by PLIP NAG.20: 1 residues within 4Å: Chain D: N.640 Ligand excluded by PLIP NAG.21: 1 residues within 4Å: Chain D: N.692 Ligand excluded by PLIP NAG.22: 3 residues within 4Å: Chain D: A.689, E.1055, N.1057 Ligand excluded by PLIP NAG.23: 1 residues within 4Å: Chain D: N.1117 Ligand excluded by PLIP NAG.24: 3 residues within 4Å: Chain E: N.106, T.108, N.109 Ligand excluded by PLIP NAG.25: 2 residues within 4Å: Chain E: N.147, N.148 Ligand excluded by PLIP NAG.26: 7 residues within 4Å: Chain D: R.440, K.441, S.442, K.445 Chain E: T.92, N.217, T.219 Ligand excluded by PLIP NAG.27: 3 residues within 4Å: Chain D: K.541 Chain E: E.264, N.265 Ligand excluded by PLIP NAG.28: 2 residues within 4Å: Chain E: N.314, Q.563 Ligand excluded by PLIP NAG.29: 2 residues within 4Å: Chain E: H.322, N.326 Ligand excluded by PLIP NAG.30: 2 residues within 4Å: Chain E: N.599 Chain F: I.817 Ligand excluded by PLIP NAG.31: 1 residues within 4Å: Chain E: N.640 Ligand excluded by PLIP NAG.32: 3 residues within 4Å: Chain E: Y.690, S.691, N.692 Ligand excluded by PLIP NAG.33: 3 residues within 4Å: Chain E: A.689, E.1055, N.1057 Ligand excluded by PLIP NAG.34: 1 residues within 4Å: Chain E: N.1117 Ligand excluded by PLIP NAG.35: 3 residues within 4Å: Chain F: N.106, T.108, N.109 Ligand excluded by PLIP NAG.36: 2 residues within 4Å: Chain F: N.147, N.148 Ligand excluded by PLIP NAG.37: 8 residues within 4Å: Chain E: R.440, K.441, S.442, K.443, K.445, E.448 Chain F: T.92, N.217 Ligand excluded by PLIP NAG.38: 3 residues within 4Å: Chain E: K.541 Chain F: E.264, N.265 Ligand excluded by PLIP NAG.39: 2 residues within 4Å: Chain F: N.314, Q.563 Ligand excluded by PLIP NAG.40: 3 residues within 4Å: Chain F: H.322, N.326, N.353 Ligand excluded by PLIP NAG.41: 2 residues within 4Å: Chain D: I.817 Chain F: N.599 Ligand excluded by PLIP NAG.42: 1 residues within 4Å: Chain F: N.640 Ligand excluded by PLIP NAG.43: 3 residues within 4Å: Chain F: Y.690, S.691, N.692 Ligand excluded by PLIP NAG.44: 2 residues within 4Å: Chain F: E.1055, N.1057 Ligand excluded by PLIP NAG.45: 1 residues within 4Å: Chain F: N.1117 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

2024-08-28

Peptides

Nanosota-5: ABC
Spike glycoprotein: DEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
M

B
N

C
O

D
A

E
B

F
C

Nanosota-5

Spike glycoprotein

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