SMTL ID : 8y4c.1

BA.2.86 S-trimer in complex with Nab XGv280

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-mer

Ligands

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

NAG.1: 2 residues within 4Å: Chain A: Y.29, N.62 Ligand excluded by PLIP NAG.2: 4 residues within 4Å: Chain A: N.121, A.122, N.124, V.169 Ligand excluded by PLIP NAG.3: 2 residues within 4Å: Chain A: Q.114, N.163 Ligand excluded by PLIP NAG.4: 3 residues within 4Å: Chain A: N.231 Chain B: V.104, V.105 Ligand excluded by PLIP NAG.5: 1 residues within 4Å: Chain A: N.242 Ligand excluded by PLIP NAG.6: 2 residues within 4Å: Chain A: N.277, N.279 Ligand excluded by PLIP NAG.7: 3 residues within 4Å: Chain A: N.328, Q.576, L.578 Ligand excluded by PLIP NAG.8: 4 residues within 4Å: Chain A: F.339, N.340, F.368, W.433 Ligand excluded by PLIP NAG.9: 2 residues within 4Å: Chain A: N.351, T.353 Ligand excluded by PLIP NAG.10: 2 residues within 4Å: Chain A: N.599, T.600 Ligand excluded by PLIP NAG.11: 1 residues within 4Å: Chain A: N.612 Ligand excluded by PLIP NAG.12: 1 residues within 4Å: Chain A: N.653 Ligand excluded by PLIP NAG.13: 3 residues within 4Å: Chain A: S.704, N.705 Chain D: Y.792 Ligand excluded by PLIP NAG.14: 3 residues within 4Å: Chain A: N.713, L.918, Q.922 Ligand excluded by PLIP NAG.15: 3 residues within 4Å: Chain A: N.797, S.799, Q.800 Ligand excluded by PLIP NAG.16: 1 residues within 4Å: Chain A: N.1070 Ligand excluded by PLIP NAG.17: 4 residues within 4Å: Chain A: N.1094, T.1096, H.1097, F.1099 Ligand excluded by PLIP NAG.18: 1 residues within 4Å: Chain A: N.1130 Ligand excluded by PLIP NAG.19: 2 residues within 4Å: Chain D: Y.29, N.62 Ligand excluded by PLIP NAG.20: 4 residues within 4Å: Chain D: N.121, A.122, N.124, V.169 Ligand excluded by PLIP NAG.21: 2 residues within 4Å: Chain D: Q.114, N.163 Ligand excluded by PLIP NAG.22: 3 residues within 4Å: Chain D: N.231 Chain E: V.104, V.105 Ligand excluded by PLIP NAG.23: 1 residues within 4Å: Chain D: N.242 Ligand excluded by PLIP NAG.24: 2 residues within 4Å: Chain D: N.277, N.279 Ligand excluded by PLIP NAG.25: 3 residues within 4Å: Chain D: N.328, Q.576, L.578 Ligand excluded by PLIP NAG.26: 4 residues within 4Å: Chain D: F.339, N.340, F.368, W.433 Ligand excluded by PLIP NAG.27: 2 residues within 4Å: Chain D: N.351, T.353 Ligand excluded by PLIP NAG.28: 2 residues within 4Å: Chain D: N.599, T.600 Ligand excluded by PLIP NAG.29: 1 residues within 4Å: Chain D: N.612 Ligand excluded by PLIP NAG.30: 1 residues within 4Å: Chain D: N.653 Ligand excluded by PLIP NAG.31: 3 residues within 4Å: Chain D: S.704, N.705 Chain G: Y.792 Ligand excluded by PLIP NAG.32: 3 residues within 4Å: Chain D: N.713, L.918, Q.922 Ligand excluded by PLIP NAG.33: 3 residues within 4Å: Chain D: N.797, S.799, Q.800 Ligand excluded by PLIP NAG.34: 2 residues within 4Å: Chain D: N.1070, F.1071 Ligand excluded by PLIP NAG.35: 4 residues within 4Å: Chain D: N.1094, T.1096, H.1097, F.1099 Ligand excluded by PLIP NAG.36: 1 residues within 4Å: Chain D: N.1130 Ligand excluded by PLIP NAG.37: 3 residues within 4Å: Chain G: Y.29, N.62 Chain I: S.96 Ligand excluded by PLIP NAG.38: 4 residues within 4Å: Chain G: N.121, A.122, N.124, V.169 Ligand excluded by PLIP NAG.39: 2 residues within 4Å: Chain G: Q.114, N.163 Ligand excluded by PLIP NAG.40: 3 residues within 4Å: Chain G: N.231 Chain H: V.104, V.105 Ligand excluded by PLIP NAG.41: 1 residues within 4Å: Chain G: N.242 Ligand excluded by PLIP NAG.42: 2 residues within 4Å: Chain G: N.277, N.279 Ligand excluded by PLIP NAG.43: 3 residues within 4Å: Chain G: N.328, Q.576, L.578 Ligand excluded by PLIP NAG.44: 4 residues within 4Å: Chain G: F.339, N.340, F.368, W.433 Ligand excluded by PLIP NAG.45: 2 residues within 4Å: Chain G: N.351, T.353 Ligand excluded by PLIP NAG.46: 2 residues within 4Å: Chain G: N.599, T.600 Ligand excluded by PLIP NAG.47: 1 residues within 4Å: Chain G: N.612 Ligand excluded by PLIP NAG.48: 1 residues within 4Å: Chain G: N.653 Ligand excluded by PLIP NAG.49: 3 residues within 4Å: Chain A: Y.792 Chain G: S.704, N.705 Ligand excluded by PLIP NAG.50: 3 residues within 4Å: Chain G: N.713, L.918, Q.922 Ligand excluded by PLIP NAG.51: 3 residues within 4Å: Chain G: N.797, S.799, Q.800 Ligand excluded by PLIP NAG.52: 2 residues within 4Å: Chain G: N.1070, F.1071 Ligand excluded by PLIP NAG.53: 4 residues within 4Å: Chain G: N.1094, T.1096, H.1097, F.1099 Ligand excluded by PLIP NAG.54: 1 residues within 4Å: Chain G: N.1130 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhu, Q. et al., Enhancing RBD exposure and S1 shedding by an extremely conserved SARS-CoV-2 NTD epitope. Signal Transduct Target Ther (2024)

Release Date

2024-09-04

Peptides

Spike glycoprotein: ADG
XGv280 Heavy chain: BEH
XGv280 Light chain: CFI

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

D
B

G
C

B
H

E
D

H
E

C
L

F
F

I
G

Spike glycoprotein

XGv280 Heavy chain

XGv280 Light chain

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