SMTL ID : 7y21.1

S-ECD (Omicron BA.5) in complex with PD of ACE2

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-mer

Ligands

38 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: 3 residues within 4Å: Chain A: N.327, Q.576, L.578 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.578 NAG-NAG.2: 3 residues within 4Å: Chain A: D.335, N.339, F.367 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 2 residues within 4Å: Chain A: N.705, I.1126 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 4 residues within 4Å: Chain A: N.713, L.918, Q.922, Q.1067 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.918, A:Q.922 NAG-NAG.5: 3 residues within 4Å: Chain A: N.797, S.799, Q.800 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 3 residues within 4Å: Chain A: A.702, E.1068, N.1070 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 3 residues within 4Å: Chain A: N.1094, T.1096, H.1097 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 1 residues within 4Å: Chain A: N.1130 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 1 residues within 4Å: Chain B: N.327 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 3 residues within 4Å: Chain B: D.335, N.339, F.367 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 3 residues within 4Å: Chain B: N.713, L.918, Q.1067 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 1 residues within 4Å: Chain B: N.797 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 4 residues within 4Å: Chain B: S.700, A.702, E.1068, N.1070 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:A.702 NAG-NAG.14: 3 residues within 4Å: Chain B: N.1094, T.1096, H.1097 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 1 residues within 4Å: Chain B: N.1130 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 2 residues within 4Å: Chain C: N.327, Q.576 No protein-ligand interaction detected (PLIP) NAG-NAG.17: 3 residues within 4Å: Chain C: D.335, N.339, F.367 No protein-ligand interaction detected (PLIP) NAG-NAG.18: 1 residues within 4Å: Chain C: N.705 No protein-ligand interaction detected (PLIP) NAG-NAG.19: 3 residues within 4Å: Chain C: N.713, L.918, Q.922 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:L.918 NAG-NAG.20: 3 residues within 4Å: Chain C: N.797, S.799, Q.800 No protein-ligand interaction detected (PLIP) NAG-NAG.21: 3 residues within 4Å: Chain C: A.702, E.1068, N.1070 No protein-ligand interaction detected (PLIP) NAG-NAG.22: 3 residues within 4Å: Chain C: N.1094, T.1096, H.1097 No protein-ligand interaction detected (PLIP) NAG-NAG.23: 1 residues within 4Å: Chain C: N.1130 No protein-ligand interaction detected (PLIP) NAG-NAG.24: 4 residues within 4Å: Chain D: N.54, T.56, E.58, Q.341 No protein-ligand interaction detected (PLIP) NAG-NAG.25: 3 residues within 4Å: Chain D: K.27, N.91, T.93 No protein-ligand interaction detected (PLIP) NAG-NAG.26: 4 residues within 4Å: Chain D: Q.82, Q.102, N.104, H.196 No protein-ligand interaction detected (PLIP) NAG-NAG.27: 3 residues within 4Å: Chain D: F.286, N.433, W.595 No protein-ligand interaction detected (PLIP) NAG-NAG.28: 2 residues within 4Å: Chain D: S.421, N.547 No protein-ligand interaction detected (PLIP) NAG-NAG.29: 4 residues within 4Å: Chain E: N.54, T.56, E.58, Q.341 No protein-ligand interaction detected (PLIP) NAG-NAG.30: 3 residues within 4Å: Chain E: K.27, N.91, T.93 No protein-ligand interaction detected (PLIP) NAG-NAG.31: 4 residues within 4Å: Chain E: Q.82, Q.102, N.104, H.196 No protein-ligand interaction detected (PLIP) NAG-NAG.32: 3 residues within 4Å: Chain E: F.286, N.433, W.595 No protein-ligand interaction detected (PLIP) NAG-NAG.33: 2 residues within 4Å: Chain E: S.421, N.547 No protein-ligand interaction detected (PLIP) NAG-NAG.34: 4 residues within 4Å: Chain F: N.54, T.56, E.58, Q.341 No protein-ligand interaction detected (PLIP) NAG-NAG.35: 3 residues within 4Å: Chain F: K.27, N.91, T.93 No protein-ligand interaction detected (PLIP) NAG-NAG.36: 4 residues within 4Å: Chain F: Q.82, Q.102, N.104, H.196 No protein-ligand interaction detected (PLIP) NAG-NAG.37: 3 residues within 4Å: Chain F: F.286, N.433, W.595 No protein-ligand interaction detected (PLIP) NAG-NAG.38: 2 residues within 4Å: Chain F: S.421, N.547 No protein-ligand interaction detected (PLIP)

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

NAG.39: 3 residues within 4Å: Chain A: Y.26, N.28, N.59 Ligand excluded by PLIP NAG.40: 3 residues within 4Å: Chain A: N.118, T.120, V.123 Ligand excluded by PLIP NAG.41: 1 residues within 4Å: Chain A: N.161 Ligand excluded by PLIP NAG.42: 2 residues within 4Å: Chain A: G.228, N.230 Ligand excluded by PLIP NAG.43: 2 residues within 4Å: Chain A: N.278 Chain C: K.554 Ligand excluded by PLIP NAG.44: 1 residues within 4Å: Chain A: N.599 Ligand excluded by PLIP NAG.45: 2 residues within 4Å: Chain A: N.612, Q.640 Ligand excluded by PLIP NAG.46: 2 residues within 4Å: Chain A: Y.651, N.653 Ligand excluded by PLIP NAG.47: 2 residues within 4Å: Chain B: Y.26, N.59 Ligand excluded by PLIP NAG.48: 3 residues within 4Å: Chain B: N.118, T.120, V.123 Ligand excluded by PLIP NAG.49: 1 residues within 4Å: Chain B: N.161 Ligand excluded by PLIP NAG.50: 2 residues within 4Å: Chain B: G.228, N.230 Ligand excluded by PLIP NAG.51: 2 residues within 4Å: Chain A: K.554 Chain B: N.278 Ligand excluded by PLIP NAG.52: 1 residues within 4Å: Chain B: N.599 Ligand excluded by PLIP NAG.53: 2 residues within 4Å: Chain B: N.612, Q.640 Ligand excluded by PLIP NAG.54: 2 residues within 4Å: Chain B: Y.651, N.653 Ligand excluded by PLIP NAG.55: 2 residues within 4Å: Chain B: N.705 Chain C: I.790 Ligand excluded by PLIP NAG.56: 3 residues within 4Å: Chain C: Y.26, N.28, N.59 Ligand excluded by PLIP NAG.57: 3 residues within 4Å: Chain C: N.118, T.120, V.123 Ligand excluded by PLIP NAG.58: 1 residues within 4Å: Chain C: N.161 Ligand excluded by PLIP NAG.59: 2 residues within 4Å: Chain C: G.228, N.230 Ligand excluded by PLIP NAG.60: 2 residues within 4Å: Chain B: K.554 Chain C: N.278 Ligand excluded by PLIP NAG.61: 1 residues within 4Å: Chain C: N.599 Ligand excluded by PLIP NAG.62: 2 residues within 4Å: Chain C: N.612, Q.640 Ligand excluded by PLIP NAG.63: 1 residues within 4Å: Chain C: N.653 Ligand excluded by PLIP NAG.64: 1 residues within 4Å: Chain D: N.323 Ligand excluded by PLIP NAG.65: 1 residues within 4Å: Chain E: N.323 Ligand excluded by PLIP NAG.66: 1 residues within 4Å: Chain F: N.323 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Li, Y. et al., Structural Basis for the Enhanced Infectivity and Immune Evasion of Omicron Subvariants. Viruses (2023)

Release Date

2023-08-09

Peptides

Spike glycoprotein: ABC
Processed angiotensin-converting enzyme 2: DEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
F

F
H

Spike glycoprotein

Processed angiotensin-converting enzyme 2

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