SMTL ID : 7yqx.1

SARS-CoV-2 BA.2.75 S Trimer in complex with S309 (state1)

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY 3.72 Å

Oligo State

hetero-3-2-2-mer

Ligands

9 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.714, L.919 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 4 residues within 4Å: Chain A: N.798, S.800, Q.801, G.929 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 2 residues within 4Å: Chain A: A.703, N.1071 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 1 residues within 4Å: Chain B: N.714 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 2 residues within 4Å: Chain B: N.798, Q.801 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 2 residues within 4Å: Chain B: A.703, N.1071 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 3 residues within 4Å: Chain C: N.714, Q.923, Q.1068 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 3 residues within 4Å: Chain C: N.798, S.800, Q.801 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 2 residues within 4Å: Chain C: A.703, N.1071 No protein-ligand interaction detected (PLIP)

2 x NAG- NAG- BMA- FUC: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-FUC.4: 10 residues within 4Å: Chain A: H.336, F.339, N.340, F.368 Chain F: Y.100, D.115 Chain G: L.47, Y.50, R.55, A.56 5 PLIP interactions: 2 interactions with chain F, 3 interactions with chain G Hydrogen bonds: F:D.115, F:D.115 Hydrophobic interactions: G:L.47, G:Y.50, G:A.56 NAG-NAG-BMA-FUC.8: 8 residues within 4Å: Chain B: H.336, F.339, N.340 Chain D: Y.32, Y.100, D.115 Chain E: Y.50, R.55 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:D.115

45 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)(Non-covalent)

NAG.12: 4 residues within 4Å: Chain A: F.56, N.58, S.254, W.255 Ligand excluded by PLIP NAG.13: 1 residues within 4Å: Chain A: N.71 Ligand excluded by PLIP NAG.14: 3 residues within 4Å: Chain A: N.119, A.120, N.122 Ligand excluded by PLIP NAG.15: 2 residues within 4Å: Chain A: N.146, R.149 Ligand excluded by PLIP NAG.16: 2 residues within 4Å: Chain A: N.161, N.162 Ligand excluded by PLIP NAG.17: 7 residues within 4Å: Chain A: T.105, N.231, T.233 Chain C: R.454, S.456, E.462, D.464 Ligand excluded by PLIP NAG.18: 3 residues within 4Å: Chain A: N.277, E.278, N.279 Ligand excluded by PLIP NAG.19: 10 residues within 4Å: Chain A: Q.406, A.408, G.410, Q.411, T.412, A.416, K.421, L.422, D.424, P.460 Ligand excluded by PLIP NAG.20: 1 residues within 4Å: Chain A: N.600 Ligand excluded by PLIP NAG.21: 2 residues within 4Å: Chain A: N.613, T.615 Ligand excluded by PLIP NAG.22: 2 residues within 4Å: Chain A: Y.652, N.654 Ligand excluded by PLIP NAG.23: 2 residues within 4Å: Chain A: S.705, N.706 Ligand excluded by PLIP NAG.24: 4 residues within 4Å: Chain A: N.1095, T.1097, H.1098, F.1100 Ligand excluded by PLIP NAG.25: 1 residues within 4Å: Chain A: N.1131 Ligand excluded by PLIP NAG.26: 1 residues within 4Å: Chain A: N.328 Ligand excluded by PLIP NAG.27: 2 residues within 4Å: Chain B: Y.25, N.58 Ligand excluded by PLIP NAG.28: 2 residues within 4Å: Chain B: T.70, N.71 Ligand excluded by PLIP NAG.29: 1 residues within 4Å: Chain B: N.119 Ligand excluded by PLIP NAG.30: 3 residues within 4Å: Chain B: Y.141, N.146, K.147 Ligand excluded by PLIP NAG.31: 2 residues within 4Å: Chain B: N.161, N.162 Ligand excluded by PLIP NAG.32: 3 residues within 4Å: Chain B: T.105, N.231, T.233 Ligand excluded by PLIP NAG.33: 3 residues within 4Å: Chain A: K.555 Chain B: E.278, N.279 Ligand excluded by PLIP NAG.34: 1 residues within 4Å: Chain B: N.328 Ligand excluded by PLIP NAG.35: 1 residues within 4Å: Chain B: N.600 Ligand excluded by PLIP NAG.36: 4 residues within 4Å: Chain B: N.613, T.615, E.616 Chain C: Q.833 Ligand excluded by PLIP NAG.37: 1 residues within 4Å: Chain B: N.654 Ligand excluded by PLIP NAG.38: 3 residues within 4Å: Chain B: S.705, N.706 Chain C: Y.793 Ligand excluded by PLIP NAG.39: 4 residues within 4Å: Chain B: N.1095, T.1097, H.1098, F.1100 Ligand excluded by PLIP NAG.40: 1 residues within 4Å: Chain B: N.1131 Ligand excluded by PLIP NAG.41: 2 residues within 4Å: Chain C: Y.25, N.58 Ligand excluded by PLIP NAG.42: 1 residues within 4Å: Chain C: N.71 Ligand excluded by PLIP NAG.43: 5 residues within 4Å: Chain C: N.119, A.120, T.121, N.122, V.124 Ligand excluded by PLIP NAG.44: 2 residues within 4Å: Chain C: N.146, K.147 Ligand excluded by PLIP NAG.45: 2 residues within 4Å: Chain C: N.161, N.162 Ligand excluded by PLIP NAG.46: 5 residues within 4Å: Chain B: E.462, D.464 Chain C: T.105, N.231, T.233 Ligand excluded by PLIP NAG.47: 2 residues within 4Å: Chain C: E.278, N.279 Ligand excluded by PLIP NAG.48: 3 residues within 4Å: Chain C: N.328, P.576, Q.577 Ligand excluded by PLIP NAG.49: 3 residues within 4Å: Chain C: F.339, N.340, F.368 Ligand excluded by PLIP NAG.50: 1 residues within 4Å: Chain C: N.600 Ligand excluded by PLIP NAG.51: 4 residues within 4Å: Chain A: I.831, Q.833 Chain C: N.613, T.615 Ligand excluded by PLIP NAG.52: 1 residues within 4Å: Chain C: N.654 Ligand excluded by PLIP NAG.53: 2 residues within 4Å: Chain A: I.791 Chain C: N.706 Ligand excluded by PLIP NAG.54: 4 residues within 4Å: Chain C: N.1095, T.1097, H.1098, F.1100 Ligand excluded by PLIP NAG.55: 1 residues within 4Å: Chain C: N.1131 Ligand excluded by PLIP NAG.56: 7 residues within 4Å: Chain B: A.341, L.438 Chain D: I.111 Chain E: T.32, Y.50, G.51, S.54 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: ABC
S309 heavy chain: DF
S309 light chain: EG

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
H

F
I

E
F

G
G

Spike glycoprotein

S309 heavy chain

S309 light chain

Related Entries With Identical Sequence