SMTL ID : 8i9b.1

S-ECD (Omicron BA.2.75) in complex with PD of ACE2

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-mer

Ligands

37 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: 4 residues within 4Å: Chain A: N.329, P.577, Q.578, L.580 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 2 residues within 4Å: Chain A: N.341, F.369 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 4 residues within 4Å: Chain A: N.715, L.920, Q.924, Q.1069 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.920 NAG-NAG.4: 3 residues within 4Å: Chain A: A.704, E.1070, N.1072 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 3 residues within 4Å: Chain A: N.1096, T.1098, F.1101 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 1 residues within 4Å: Chain A: N.1132 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 3 residues within 4Å: Chain B: N.329, P.577, Q.578 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 2 residues within 4Å: Chain B: N.341, F.369 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 2 residues within 4Å: Chain B: N.707, G.1129 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 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.11: 3 residues within 4Å: Chain B: N.799, S.801, Q.802 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 4 residues within 4Å: Chain B: A.704, E.1070, K.1071, N.1072 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:A.704 NAG-NAG.13: 4 residues within 4Å: Chain B: N.1096, T.1098, H.1099, F.1101 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 1 residues within 4Å: Chain B: N.1132 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 2 residues within 4Å: Chain C: N.329, Q.578 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 1 residues within 4Å: Chain C: N.341 No protein-ligand interaction detected (PLIP) NAG-NAG.17: 1 residues within 4Å: Chain C: N.707 No protein-ligand interaction detected (PLIP) NAG-NAG.18: 5 residues within 4Å: Chain C: N.715, L.920, N.923, Q.924, Q.1069 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:L.920, C:N.923 NAG-NAG.19: 2 residues within 4Å: Chain C: N.799, S.801 No protein-ligand interaction detected (PLIP) NAG-NAG.20: 3 residues within 4Å: Chain C: A.704, E.1070, N.1072 No protein-ligand interaction detected (PLIP) NAG-NAG.21: 4 residues within 4Å: Chain C: N.1096, T.1098, H.1099, F.1101 No protein-ligand interaction detected (PLIP) NAG-NAG.22: 1 residues within 4Å: Chain C: N.1132 No protein-ligand interaction detected (PLIP) NAG-NAG.23: 5 residues within 4Å: Chain D: N.54, T.56, E.58, N.59, Q.341 No protein-ligand interaction detected (PLIP) NAG-NAG.24: 2 residues within 4Å: Chain D: K.27, N.91 No protein-ligand interaction detected (PLIP) NAG-NAG.25: 3 residues within 4Å: Chain D: Q.82, Q.102, N.104 No protein-ligand interaction detected (PLIP) NAG-NAG.26: 3 residues within 4Å: Chain D: F.286, N.433, W.595 No protein-ligand interaction detected (PLIP) NAG-NAG.27: 4 residues within 4Å: Chain D: S.421, D.544, S.546, N.547 No protein-ligand interaction detected (PLIP) NAG-NAG.28: 5 residues within 4Å: Chain E: N.54, T.56, E.58, N.59, Q.341 No protein-ligand interaction detected (PLIP) NAG-NAG.29: 2 residues within 4Å: Chain E: K.27, N.91 No protein-ligand interaction detected (PLIP) NAG-NAG.30: 3 residues within 4Å: Chain E: Q.82, Q.102, N.104 No protein-ligand interaction detected (PLIP) NAG-NAG.31: 3 residues within 4Å: Chain E: F.286, N.433, W.595 No protein-ligand interaction detected (PLIP) NAG-NAG.32: 4 residues within 4Å: Chain E: S.421, D.544, S.546, N.547 No protein-ligand interaction detected (PLIP) NAG-NAG.33: 5 residues within 4Å: Chain F: N.54, T.56, E.58, N.59, Q.341 No protein-ligand interaction detected (PLIP) NAG-NAG.34: 2 residues within 4Å: Chain F: K.27, N.91 No protein-ligand interaction detected (PLIP) NAG-NAG.35: 3 residues within 4Å: Chain F: Q.82, Q.102, N.104 No protein-ligand interaction detected (PLIP) NAG-NAG.36: 3 residues within 4Å: Chain F: F.286, N.433, W.595 No protein-ligand interaction detected (PLIP) NAG-NAG.37: 4 residues within 4Å: Chain F: S.421, D.544, S.546, N.547 No protein-ligand interaction detected (PLIP)

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

NAG.38: 2 residues within 4Å: Chain A: Y.26, N.59 Ligand excluded by PLIP NAG.39: 3 residues within 4Å: Chain A: N.120, T.122, V.125 Ligand excluded by PLIP NAG.40: 2 residues within 4Å: Chain A: E.130, N.163 Ligand excluded by PLIP NAG.41: 2 residues within 4Å: Chain A: G.230, N.232 Ligand excluded by PLIP NAG.42: 3 residues within 4Å: Chain A: N.278, E.279, N.280 Ligand excluded by PLIP NAG.43: 2 residues within 4Å: Chain A: N.601, T.602 Ligand excluded by PLIP NAG.44: 1 residues within 4Å: Chain A: N.614 Ligand excluded by PLIP NAG.45: 1 residues within 4Å: Chain A: N.655 Ligand excluded by PLIP NAG.46: 2 residues within 4Å: Chain A: N.707, G.1129 Ligand excluded by PLIP NAG.47: 1 residues within 4Å: Chain A: N.799 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: 2 residues within 4Å: Chain B: E.130, N.163 Ligand excluded by PLIP NAG.51: 2 residues within 4Å: Chain B: G.230, N.232 Ligand excluded by PLIP NAG.52: 3 residues within 4Å: Chain B: N.278, E.279, N.280 Ligand excluded by PLIP NAG.53: 2 residues within 4Å: Chain B: N.601, T.602 Ligand excluded by PLIP NAG.54: 1 residues within 4Å: Chain B: N.614 Ligand excluded by PLIP NAG.55: 1 residues within 4Å: Chain B: N.655 Ligand excluded by PLIP NAG.56: 2 residues within 4Å: Chain C: Y.26, 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: 2 residues within 4Å: Chain C: E.130, N.163 Ligand excluded by PLIP NAG.59: 2 residues within 4Å: Chain C: G.230, N.232 Ligand excluded by PLIP NAG.60: 3 residues within 4Å: Chain C: N.278, E.279, N.280 Ligand excluded by PLIP NAG.61: 2 residues within 4Å: Chain C: N.601, T.602 Ligand excluded by PLIP NAG.62: 1 residues within 4Å: Chain C: N.614 Ligand excluded by PLIP NAG.63: 1 residues within 4Å: Chain C: N.655 Ligand excluded by PLIP NAG.64: 2 residues within 4Å: Chain D: V.317, N.323 Ligand excluded by PLIP NAG.65: 2 residues within 4Å: Chain E: V.317, N.323 Ligand excluded by PLIP NAG.66: 2 residues within 4Å: Chain F: V.317, N.323 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Li, Y. et al., Cryo-EM structures of SARS-CoV-2 BA.2-derived subvariants spike in complex with ACE2 receptor. Cell Discov (2023)

Release Date

2024-02-07

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
F

E
D

F
E

Spike glycoprotein

Processed angiotensin-converting enzyme 2

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