SMTL ID : 8y4a.1

BA.2.86 S-trimer in complex with Nab XG2v046

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-2-2-mer

Ligands

9 x NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-BMA.1: 3 residues within 4Å: Chain A: N.797, S.799, Q.800 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.799 NAG-BMA.2: 4 residues within 4Å: Chain A: N.713, L.918, Q.922, Q.1067 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.1067 NAG-BMA.3: 3 residues within 4Å: Chain A: N.1094, T.1096, H.1097 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:T.1096 Hydrogen bonds: A:N.1094 NAG-BMA.6: 4 residues within 4Å: Chain B: N.277, E.278, N.279 Chain C: K.554 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain B Hydrogen bonds: C:K.554, B:N.277, B:E.278 NAG-BMA.7: 3 residues within 4Å: Chain B: N.797, S.799, Q.800 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.799 NAG-BMA.8: 1 residues within 4Å: Chain B: N.713 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.713 NAG-BMA.11: 3 residues within 4Å: Chain C: N.797, S.799, Q.800 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:N.797, C:S.799, C:Q.800 NAG-BMA.12: 1 residues within 4Å: Chain C: N.713 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.713 NAG-BMA.13: 5 residues within 4Å: Chain C: N.1094, G.1095, T.1096, H.1097, F.1099 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:G.1095, C:T.1096

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

NAG-NAG.4: 1 residues within 4Å: Chain A: N.1130 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 2 residues within 4Å: Chain B: N.1094, H.1097 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 1 residues within 4Å: Chain B: N.1130 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 1 residues within 4Å: Chain C: N.1130 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(8-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA.5: 4 residues within 4Å: Chain A: N.163 Chain B: E.337, N.351, T.353 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.337

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

NAG.15: 4 residues within 4Å: Chain A: N.612 Chain C: K.831, Y.833, G.834 Ligand excluded by PLIP NAG.16: 1 residues within 4Å: Chain A: N.653 Ligand excluded by PLIP NAG.17: 3 residues within 4Å: Chain A: S.704, N.705 Chain C: Y.792 Ligand excluded by PLIP NAG.18: 2 residues within 4Å: Chain A: E.1068, N.1070 Ligand excluded by PLIP NAG.19: 1 residues within 4Å: Chain A: N.599 Ligand excluded by PLIP NAG.20: 2 residues within 4Å: Chain A: S.61, N.62 Ligand excluded by PLIP NAG.21: 4 residues within 4Å: Chain A: N.121, T.123, N.124, F.126 Ligand excluded by PLIP NAG.22: 5 residues within 4Å: Chain A: I.230, N.231 Chain B: F.461, E.462, R.463 Ligand excluded by PLIP NAG.23: 2 residues within 4Å: Chain A: N.242, R.243 Ligand excluded by PLIP NAG.24: 2 residues within 4Å: Chain A: N.277, N.279 Ligand excluded by PLIP NAG.25: 2 residues within 4Å: Chain A: N.328, V.329 Ligand excluded by PLIP NAG.26: 3 residues within 4Å: Chain A: H.336, N.340, F.368 Ligand excluded by PLIP NAG.27: 4 residues within 4Å: Chain A: E.337, R.343, N.351, T.353 Ligand excluded by PLIP NAG.28: 2 residues within 4Å: Chain B: N.612, T.614 Ligand excluded by PLIP NAG.29: 2 residues within 4Å: Chain B: Y.651, N.653 Ligand excluded by PLIP NAG.30: 4 residues within 4Å: Chain A: I.790 Chain B: Y.703, S.704, N.705 Ligand excluded by PLIP NAG.31: 2 residues within 4Å: Chain B: E.1068, N.1070 Ligand excluded by PLIP NAG.32: 3 residues within 4Å: Chain B: N.340, T.342, F.368 Ligand excluded by PLIP NAG.33: 2 residues within 4Å: Chain B: N.328, Q.576 Ligand excluded by PLIP NAG.34: 2 residues within 4Å: Chain B: F.60, N.62 Ligand excluded by PLIP NAG.35: 2 residues within 4Å: Chain B: N.121, T.123 Ligand excluded by PLIP NAG.36: 2 residues within 4Å: Chain B: Q.114, N.163 Ligand excluded by PLIP NAG.37: 3 residues within 4Å: Chain B: G.229, I.230, N.231 Ligand excluded by PLIP NAG.38: 2 residues within 4Å: Chain B: N.242, R.243 Ligand excluded by PLIP NAG.39: 2 residues within 4Å: Chain B: N.599, T.600 Ligand excluded by PLIP NAG.40: 3 residues within 4Å: Chain C: P.327, N.328, Q.576 Ligand excluded by PLIP NAG.41: 3 residues within 4Å: Chain B: Y.833 Chain C: N.612, T.614 Ligand excluded by PLIP NAG.42: 1 residues within 4Å: Chain C: N.653 Ligand excluded by PLIP NAG.43: 3 residues within 4Å: Chain B: Y.792 Chain C: S.704, N.705 Ligand excluded by PLIP NAG.44: 3 residues within 4Å: Chain C: A.702, E.1068, N.1070 Ligand excluded by PLIP NAG.45: 4 residues within 4Å: Chain C: R.343, A.345, N.351, T.353 Ligand excluded by PLIP NAG.46: 4 residues within 4Å: Chain C: H.336, F.339, N.340, F.368 Ligand excluded by PLIP NAG.47: 1 residues within 4Å: Chain C: N.599 Ligand excluded by PLIP NAG.48: 1 residues within 4Å: Chain C: N.62 Ligand excluded by PLIP NAG.49: 4 residues within 4Å: Chain C: N.121, T.123, N.124, F.126 Ligand excluded by PLIP NAG.50: 2 residues within 4Å: Chain C: Q.114, N.163 Ligand excluded by PLIP NAG.51: 2 residues within 4Å: Chain C: I.230, N.231 Ligand excluded by PLIP NAG.52: 2 residues within 4Å: Chain C: N.242, R.243 Ligand excluded by PLIP NAG.53: 3 residues within 4Å: Chain A: K.554 Chain C: N.277, N.279 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

2024-09-11

Peptides

Spike glycoprotein: ABC
XG2v046 Heavy chain: DF
XG2v046 Light chain: EG

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
C

C
A

D
H

F
D

E
L

G
E

Spike glycoprotein

XG2v046 Heavy chain

XG2v046 Light chain

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