SMTL ID : 7y1y.1

S-ECD (Omicron BA.2) 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: 2 residues within 4Å: Chain A: N.329, Q.578 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 2 residues within 4Å: Chain A: D.337, N.341 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 3 residues within 4Å: Chain A: N.715, L.920, Q.1069 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 1 residues within 4Å: Chain A: N.799 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 4 residues within 4Å: Chain A: S.702, A.704, E.1070, N.1072 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:A.704 NAG-NAG.6: 3 residues within 4Å: Chain A: N.1096, T.1098, H.1099 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 1 residues within 4Å: Chain A: N.1132 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 4 residues within 4Å: Chain B: N.329, P.577, Q.578, L.580 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 2 residues within 4Å: Chain B: D.337, N.341 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 1 residues within 4Å: Chain B: N.707 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 3 residues within 4Å: Chain B: N.715, L.920, Q.924 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:L.920 NAG-NAG.12: 3 residues within 4Å: Chain B: N.799, S.801, Q.802 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 3 residues within 4Å: Chain B: A.704, E.1070, N.1072 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 3 residues within 4Å: Chain B: N.1096, T.1098, H.1099 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 1 residues within 4Å: Chain B: N.1132 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 2 residues within 4Å: Chain C: N.329, Q.578 No protein-ligand interaction detected (PLIP) NAG-NAG.17: 2 residues within 4Å: Chain C: D.337, N.341 No protein-ligand interaction detected (PLIP) NAG-NAG.18: 2 residues within 4Å: Chain C: N.707, I.1128 No protein-ligand interaction detected (PLIP) NAG-NAG.19: 4 residues within 4Å: Chain C: N.715, L.920, Q.924, Q.1069 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:L.920, C:Q.924 NAG-NAG.20: 3 residues within 4Å: Chain C: N.799, S.801, Q.802 No protein-ligand interaction detected (PLIP) NAG-NAG.21: 3 residues within 4Å: Chain C: A.704, E.1070, N.1072 No protein-ligand interaction detected (PLIP) NAG-NAG.22: 3 residues within 4Å: Chain C: N.1096, T.1098, H.1099 No protein-ligand interaction detected (PLIP) NAG-NAG.23: 1 residues within 4Å: Chain C: N.1132 No protein-ligand interaction detected (PLIP) NAG-NAG.24: 5 residues within 4Å: Chain D: N.54, T.56, E.58, N.59, Q.341 No protein-ligand interaction detected (PLIP) NAG-NAG.25: 2 residues within 4Å: Chain D: N.91, T.93 No protein-ligand interaction detected (PLIP) NAG-NAG.26: 3 residues within 4Å: Chain D: Q.82, N.104, H.196 No protein-ligand interaction detected (PLIP) NAG-NAG.27: 1 residues within 4Å: Chain D: N.433 No protein-ligand interaction detected (PLIP) NAG-NAG.28: 2 residues within 4Å: Chain D: K.314, N.547 No protein-ligand interaction detected (PLIP) NAG-NAG.29: 5 residues within 4Å: Chain E: N.54, T.56, E.58, N.59, 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: 3 residues within 4Å: Chain E: Q.82, N.104, H.196 No protein-ligand interaction detected (PLIP) NAG-NAG.32: 1 residues within 4Å: Chain E: N.433 No protein-ligand interaction detected (PLIP) NAG-NAG.33: 2 residues within 4Å: Chain E: K.314, N.547 No protein-ligand interaction detected (PLIP) NAG-NAG.34: 5 residues within 4Å: Chain F: N.54, T.56, E.58, N.59, 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: 3 residues within 4Å: Chain F: Q.82, N.104, H.196 No protein-ligand interaction detected (PLIP) NAG-NAG.37: 1 residues within 4Å: Chain F: N.433 No protein-ligand interaction detected (PLIP) NAG-NAG.38: 2 residues within 4Å: Chain F: K.314, 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.120, T.122, V.125 Ligand excluded by PLIP NAG.41: 2 residues within 4Å: Chain A: E.130, N.163 Ligand excluded by PLIP NAG.42: 2 residues within 4Å: Chain A: G.230, N.232 Ligand excluded by PLIP NAG.43: 2 residues within 4Å: Chain A: N.280 Chain C: K.556 Ligand excluded by PLIP NAG.44: 1 residues within 4Å: Chain A: N.601 Ligand excluded by PLIP NAG.45: 2 residues within 4Å: Chain A: N.614, Q.642 Ligand excluded by PLIP NAG.46: 2 residues within 4Å: Chain A: Y.653, N.655 Ligand excluded by PLIP NAG.47: 2 residues within 4Å: Chain A: N.707, I.1128 Ligand excluded by PLIP NAG.48: 2 residues within 4Å: Chain B: Y.26, N.59 Ligand excluded by PLIP NAG.49: 3 residues within 4Å: Chain B: N.120, T.122, V.125 Ligand excluded by PLIP NAG.50: 1 residues within 4Å: Chain B: N.163 Ligand excluded by PLIP NAG.51: 2 residues within 4Å: Chain B: G.230, N.232 Ligand excluded by PLIP NAG.52: 2 residues within 4Å: Chain A: K.556 Chain B: N.280 Ligand excluded by PLIP NAG.53: 1 residues within 4Å: Chain B: N.601 Ligand excluded by PLIP NAG.54: 2 residues within 4Å: Chain B: N.614, Q.642 Ligand excluded by PLIP NAG.55: 1 residues within 4Å: Chain B: N.655 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.120, T.122, V.125 Ligand excluded by PLIP NAG.58: 3 residues within 4Å: Chain C: Q.113, N.163, T.165 Ligand excluded by PLIP NAG.59: 2 residues within 4Å: Chain C: G.230, N.232 Ligand excluded by PLIP NAG.60: 2 residues within 4Å: Chain B: K.556 Chain C: N.280 Ligand excluded by PLIP NAG.61: 1 residues within 4Å: Chain C: N.601 Ligand excluded by PLIP NAG.62: 2 residues within 4Å: Chain C: N.614, Q.642 Ligand excluded by PLIP NAG.63: 2 residues within 4Å: Chain C: Y.653, N.655 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

2023-07-12

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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