SMTL ID : 7yqy.1

SARS-CoV-2 BA.2.75 S Trimer in complex with S309 (state2)

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY 3.74 Å

Oligo State

hetero-3-3-3-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: 3 residues within 4Å: Chain A: N.798, S.800, Q.801 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.800, A:Q.801 NAG-NAG.3: 2 residues within 4Å: Chain A: A.703, N.1071 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 3 residues within 4Å: Chain B: N.714, L.919, Q.923 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:L.919 NAG-NAG.6: 2 residues within 4Å: Chain B: N.798, S.800 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: 2 residues within 4Å: Chain C: N.714, L.919 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)

3 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: 13 residues within 4Å: Chain A: H.336, F.339, N.340, V.364, F.368, A.369 Chain E: L.47, Y.50, R.55 Chain G: Y.32, R.98, Y.100, D.115 6 PLIP interactions: 4 interactions with chain G, 2 interactions with chain E Hydrogen bonds: G:Y.32, G:R.98, G:D.115, G:D.115 Hydrophobic interactions: E:L.47, E:Y.50 NAG-NAG-BMA-FUC.8: 8 residues within 4Å: Chain B: F.339, N.340, V.364, L.365, F.368, A.369 Chain D: Y.50 Chain F: Y.100 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:Y.50 Hydrogen bonds: D:Y.50 NAG-NAG-BMA-FUC.12: 8 residues within 4Å: Chain C: F.368, A.369, F.371 Chain H: Y.32, R.98, Y.100, D.115 Chain I: Y.50 2 PLIP interactions: 1 interactions with chain I, 1 interactions with chain C Hydrogen bonds: I:Y.50, C:A.369

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

NAG.13: 3 residues within 4Å: Chain A: Y.25, N.58, W.255 Ligand excluded by PLIP NAG.14: 1 residues within 4Å: Chain A: N.71 Ligand excluded by PLIP NAG.15: 2 residues within 4Å: Chain A: K.126, L.154 Ligand excluded by PLIP NAG.16: 3 residues within 4Å: Chain A: Y.141, K.147, R.149 Ligand excluded by PLIP NAG.17: 1 residues within 4Å: Chain A: N.279 Ligand excluded by PLIP NAG.18: 8 residues within 4Å: Chain A: A.408, P.409, G.410, Q.411, T.412, K.421, L.422, D.424 Ligand excluded by PLIP NAG.19: 1 residues within 4Å: Chain A: N.600 Ligand excluded by PLIP NAG.20: 2 residues within 4Å: Chain A: N.613, T.615 Ligand excluded by PLIP NAG.21: 1 residues within 4Å: Chain A: N.654 Ligand excluded by PLIP NAG.22: 3 residues within 4Å: Chain A: S.705, N.706 Chain B: Y.793 Ligand excluded by PLIP NAG.23: 4 residues within 4Å: Chain A: N.1095, T.1097, H.1098, F.1100 Ligand excluded by PLIP NAG.24: 1 residues within 4Å: Chain A: N.1131 Ligand excluded by PLIP NAG.25: 2 residues within 4Å: Chain A: N.328, Q.577 Ligand excluded by PLIP NAG.26: 4 residues within 4Å: Chain B: Y.25, N.58, S.254, W.255 Ligand excluded by PLIP NAG.27: 2 residues within 4Å: Chain B: T.70, N.71 Ligand excluded by PLIP NAG.28: 4 residues within 4Å: Chain B: N.118, N.119, A.120, N.122 Ligand excluded by PLIP NAG.29: 3 residues within 4Å: Chain B: Y.141, N.146, K.147 Ligand excluded by PLIP NAG.30: 2 residues within 4Å: Chain B: N.161, N.162 Ligand excluded by PLIP NAG.31: 2 residues within 4Å: Chain B: N.231, T.233 Ligand excluded by PLIP NAG.32: 2 residues within 4Å: Chain B: E.278, N.279 Ligand excluded by PLIP NAG.33: 2 residues within 4Å: Chain B: N.328, Q.577 Ligand excluded by PLIP NAG.34: 8 residues within 4Å: Chain B: W.433, N.434, S.435, N.436, K.437, L.438, D.439, R.506 Ligand excluded by PLIP NAG.35: 1 residues within 4Å: Chain B: N.600 Ligand excluded by PLIP NAG.36: 2 residues within 4Å: Chain B: N.613, T.615 Ligand excluded by PLIP NAG.37: 1 residues within 4Å: Chain B: N.654 Ligand excluded by PLIP NAG.38: 2 residues within 4Å: Chain B: S.705, N.706 Ligand excluded by PLIP NAG.39: 3 residues within 4Å: Chain B: N.1095, T.1097, H.1098 Ligand excluded by PLIP NAG.40: 1 residues within 4Å: Chain B: N.1131 Ligand excluded by PLIP NAG.41: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP NAG.42: 3 residues within 4Å: Chain C: R.454, K.459, E.462 Ligand excluded by PLIP NAG.43: 1 residues within 4Å: Chain C: N.58 Ligand excluded by PLIP NAG.44: 1 residues within 4Å: Chain C: N.71 Ligand excluded by PLIP NAG.45: 3 residues within 4Å: Chain C: N.119, A.120, N.122 Ligand excluded by PLIP NAG.46: 2 residues within 4Å: Chain C: N.146, K.147 Ligand excluded by PLIP NAG.47: 4 residues within 4Å: Chain B: Y.348, I.465 Chain C: N.161, N.162 Ligand excluded by PLIP NAG.48: 1 residues within 4Å: Chain C: N.231 Ligand excluded by PLIP NAG.49: 2 residues within 4Å: Chain C: E.278, N.279 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: F.830, I.831 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: Y.793 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: 2 residues within 4Å: Chain C: N.328, Q.577 Ligand excluded by PLIP NAG.57: 8 residues within 4Å: Chain C: F.371, W.433, K.437, L.438 Chain H: I.111 Chain I: 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 light chain: DEI
S309 heavy chain: FGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
F

E
G

I
E

F
H

G
I

H
J

Spike glycoprotein

S309 light chain

S309 heavy chain

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