SMTL ID : 7yr1.1

SARS-CoV-2 BA.2.75 S Trimer in complex with XG2v024

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-mer

Ligands

15 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: 2 residues within 4Å: Chain A: N.119, V.124 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 4 residues within 4Å: Chain A: N.277, E.278, N.279, T.281 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 3 residues within 4Å: Chain A: S.705, N.706 Chain D: Y.793 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 1 residues within 4Å: Chain A: N.1071 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 1 residues within 4Å: Chain A: N.1131 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 2 residues within 4Å: Chain D: N.119, V.124 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 4 residues within 4Å: Chain D: N.277, E.278, N.279, T.281 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 3 residues within 4Å: Chain D: S.705, N.706 Chain G: Y.793 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 1 residues within 4Å: Chain D: N.1071 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 1 residues within 4Å: Chain D: N.1131 No protein-ligand interaction detected (PLIP) NAG-NAG.17: 2 residues within 4Å: Chain G: N.119, V.124 No protein-ligand interaction detected (PLIP) NAG-NAG.18: 4 residues within 4Å: Chain G: N.277, E.278, N.279, T.281 No protein-ligand interaction detected (PLIP) NAG-NAG.19: 3 residues within 4Å: Chain A: Y.793 Chain G: S.705, N.706 No protein-ligand interaction detected (PLIP) NAG-NAG.22: 1 residues within 4Å: Chain G: N.1071 No protein-ligand interaction detected (PLIP) NAG-NAG.24: 1 residues within 4Å: Chain G: N.1131 No protein-ligand interaction detected (PLIP)

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

NAG-NAG-BMA.4: 2 residues within 4Å: Chain A: N.714, L.919 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.5: 2 residues within 4Å: Chain A: N.798, Q.801 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.7: 3 residues within 4Å: Chain A: N.1095, H.1098, F.1100 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.12: 2 residues within 4Å: Chain D: N.714, L.919 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.13: 2 residues within 4Å: Chain D: N.798, Q.801 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.15: 3 residues within 4Å: Chain D: N.1095, H.1098, F.1100 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.20: 2 residues within 4Å: Chain G: N.714, L.919 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.21: 2 residues within 4Å: Chain G: N.798, Q.801 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.23: 3 residues within 4Å: Chain G: N.1095, H.1098, F.1100 No protein-ligand interaction detected (PLIP)

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

NAG.25: 1 residues within 4Å: Chain A: N.58 Ligand excluded by PLIP NAG.26: 2 residues within 4Å: Chain A: N.161, N.162 Ligand excluded by PLIP NAG.27: 2 residues within 4Å: Chain A: N.231 Chain G: E.462 Ligand excluded by PLIP NAG.28: 2 residues within 4Å: Chain A: N.328, Q.577 Ligand excluded by PLIP NAG.29: 2 residues within 4Å: Chain A: H.336, N.340 Ligand excluded by PLIP NAG.30: 1 residues within 4Å: Chain A: N.600 Ligand excluded by PLIP NAG.31: 3 residues within 4Å: Chain A: N.613, E.616 Chain D: I.831 Ligand excluded by PLIP NAG.32: 1 residues within 4Å: Chain A: N.654 Ligand excluded by PLIP NAG.33: 1 residues within 4Å: Chain D: N.58 Ligand excluded by PLIP NAG.34: 2 residues within 4Å: Chain D: N.161, N.162 Ligand excluded by PLIP NAG.35: 2 residues within 4Å: Chain A: E.462 Chain D: N.231 Ligand excluded by PLIP NAG.36: 2 residues within 4Å: Chain D: N.328, Q.577 Ligand excluded by PLIP NAG.37: 2 residues within 4Å: Chain D: H.336, N.340 Ligand excluded by PLIP NAG.38: 1 residues within 4Å: Chain D: N.600 Ligand excluded by PLIP NAG.39: 3 residues within 4Å: Chain D: N.613, E.616 Chain G: I.831 Ligand excluded by PLIP NAG.40: 1 residues within 4Å: Chain D: N.654 Ligand excluded by PLIP NAG.41: 1 residues within 4Å: Chain G: N.58 Ligand excluded by PLIP NAG.42: 2 residues within 4Å: Chain G: N.161, N.162 Ligand excluded by PLIP NAG.43: 2 residues within 4Å: Chain D: E.462 Chain G: N.231 Ligand excluded by PLIP NAG.44: 2 residues within 4Å: Chain G: N.328, Q.577 Ligand excluded by PLIP NAG.45: 2 residues within 4Å: Chain G: H.336, N.340 Ligand excluded by PLIP NAG.46: 1 residues within 4Å: Chain G: N.600 Ligand excluded by PLIP NAG.47: 3 residues within 4Å: Chain A: I.831 Chain G: N.613, E.616 Ligand excluded by PLIP NAG.48: 1 residues within 4Å: Chain G: N.654 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cao, Y. et al., Characterization of the enhanced infectivity and antibody evasion of Omicron BA.2.75. Cell Host Microbe (2022)

Release Date

2022-10-19

Peptides

Spike glycoprotein: ADG
XG2v024 Heavy chain: BEH
XG2v024 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

XG2v024 Heavy chain

XG2v024 Light chain

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