SMTL ID : 7xid.1

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

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-2-mer

Ligands

23 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: P.327, N.328 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 3 residues within 4Å: Chain A: N.714, L.919, Q.1068 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 1 residues within 4Å: Chain A: N.798 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 4 residues within 4Å: Chain A: S.701, A.703, E.1069, N.1071 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:A.703 NAG-NAG.5: 3 residues within 4Å: Chain A: N.1095, T.1097, H.1098 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 1 residues within 4Å: Chain A: N.1131 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 3 residues within 4Å: Chain B: N.328, Q.577, L.579 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 4 residues within 4Å: Chain B: D.336, N.340, N.367 Ligands: NAG.40 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:N.367 NAG-NAG.9: 1 residues within 4Å: Chain B: N.706 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 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.11: 3 residues within 4Å: Chain B: N.798, S.800, Q.801 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 3 residues within 4Å: Chain B: N.1095, T.1097, H.1098 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 1 residues within 4Å: Chain B: N.1131 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 3 residues within 4Å: Chain C: N.328, Q.577, L.579 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 4 residues within 4Å: Chain C: D.336, N.340, N.367 Ligands: NAG.51 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:N.367 NAG-NAG.16: 2 residues within 4Å: Chain C: N.706, I.1127 No protein-ligand interaction detected (PLIP) NAG-NAG.17: 4 residues within 4Å: Chain C: N.714, L.919, Q.923, Q.1068 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:L.919, C:Q.923 NAG-NAG.18: 3 residues within 4Å: Chain C: N.798, S.800, Q.801 No protein-ligand interaction detected (PLIP) NAG-NAG.19: 3 residues within 4Å: Chain C: A.703, E.1069, N.1071 No protein-ligand interaction detected (PLIP) NAG-NAG.20: 3 residues within 4Å: Chain C: N.1095, T.1097, H.1098 No protein-ligand interaction detected (PLIP) NAG-NAG.21: 1 residues within 4Å: Chain C: N.1131 No protein-ligand interaction detected (PLIP) NAG-NAG.22: 2 residues within 4Å: Chain D: N.65, Q.352 No protein-ligand interaction detected (PLIP) NAG-NAG.23: 2 residues within 4Å: Chain E: N.65, Q.352 No protein-ligand interaction detected (PLIP)

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

NAG.24: 3 residues within 4Å: Chain A: Y.28, N.30, N.61 Ligand excluded by PLIP NAG.25: 4 residues within 4Å: Chain A: N.120, T.122, V.125, F.152 Ligand excluded by PLIP NAG.26: 1 residues within 4Å: Chain A: N.160 Ligand excluded by PLIP NAG.27: 2 residues within 4Å: Chain A: G.229, N.231 Ligand excluded by PLIP NAG.28: 2 residues within 4Å: Chain A: N.279 Chain C: K.555 Ligand excluded by PLIP NAG.29: 3 residues within 4Å: Chain A: D.336, N.340 Ligands: NAG.30 Ligand excluded by PLIP NAG.30: 1 residues within 4Å: Ligands: NAG.29 Ligand excluded by PLIP NAG.31: 1 residues within 4Å: Chain A: N.600 Ligand excluded by PLIP NAG.32: 3 residues within 4Å: Chain A: N.613, T.615, Q.641 Ligand excluded by PLIP NAG.33: 2 residues within 4Å: Chain A: Y.652, N.654 Ligand excluded by PLIP NAG.34: 3 residues within 4Å: Chain A: N.706, I.1127, G.1128 Ligand excluded by PLIP NAG.35: 3 residues within 4Å: Chain B: Y.28, N.30, N.61 Ligand excluded by PLIP NAG.36: 2 residues within 4Å: Chain B: N.120, T.122 Ligand excluded by PLIP NAG.37: 1 residues within 4Å: Chain B: N.160 Ligand excluded by PLIP NAG.38: 2 residues within 4Å: Chain B: G.229, N.231 Ligand excluded by PLIP NAG.39: 1 residues within 4Å: Chain B: N.279 Ligand excluded by PLIP NAG.40: 1 residues within 4Å: Ligands: NAG-NAG.8 Ligand excluded by PLIP NAG.41: 1 residues within 4Å: Chain B: N.600 Ligand excluded by PLIP NAG.42: 3 residues within 4Å: Chain B: N.613, T.615, Q.641 Ligand excluded by PLIP NAG.43: 2 residues within 4Å: Chain B: Y.652, N.654 Ligand excluded by PLIP NAG.44: 4 residues within 4Å: Chain B: A.703, E.1069, N.1071 Ligands: NAG.45 Ligand excluded by PLIP NAG.45: 1 residues within 4Å: Ligands: NAG.44 Ligand excluded by PLIP NAG.46: 3 residues within 4Å: Chain C: Y.28, N.30, N.61 Ligand excluded by PLIP NAG.47: 3 residues within 4Å: Chain C: N.120, T.122, V.125 Ligand excluded by PLIP NAG.48: 1 residues within 4Å: Chain C: N.160 Ligand excluded by PLIP NAG.49: 2 residues within 4Å: Chain C: G.229, N.231 Ligand excluded by PLIP NAG.50: 1 residues within 4Å: Chain C: N.279 Ligand excluded by PLIP NAG.51: 1 residues within 4Å: Ligands: NAG-NAG.15 Ligand excluded by PLIP NAG.52: 1 residues within 4Å: Chain C: N.600 Ligand excluded by PLIP NAG.53: 2 residues within 4Å: Chain C: N.613, Q.641 Ligand excluded by PLIP NAG.54: 2 residues within 4Å: Chain C: Y.652, N.654 Ligand excluded by PLIP NAG.55: 2 residues within 4Å: Chain D: N.102, T.104 Ligand excluded by PLIP NAG.56: 4 residues within 4Å: Chain D: Q.113, Q.114, N.115, V.119 Ligand excluded by PLIP NAG.57: 3 residues within 4Å: Chain D: E.324, V.328, N.334 Ligand excluded by PLIP NAG.58: 1 residues within 4Å: Chain D: N.444 Ligand excluded by PLIP NAG.59: 3 residues within 4Å: Chain D: S.329, N.558 Ligands: NAG.60 Ligand excluded by PLIP NAG.60: 2 residues within 4Å: Ligands: NAG.59, NAG.61 Ligand excluded by PLIP NAG.61: 1 residues within 4Å: Ligands: NAG.60 Ligand excluded by PLIP NAG.62: 2 residues within 4Å: Chain E: N.102, T.104 Ligand excluded by PLIP NAG.63: 4 residues within 4Å: Chain E: Q.113, Q.114, N.115, V.119 Ligand excluded by PLIP NAG.64: 3 residues within 4Å: Chain E: E.324, V.328, N.334 Ligand excluded by PLIP NAG.65: 1 residues within 4Å: Chain E: N.444 Ligand excluded by PLIP NAG.66: 3 residues within 4Å: Chain E: S.329, N.558 Ligands: NAG.67 Ligand excluded by PLIP NAG.67: 2 residues within 4Å: Ligands: NAG.66, NAG.68 Ligand excluded by PLIP NAG.68: 1 residues within 4Å: Ligands: NAG.67 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Li, Y. et al., Structural and functional analysis of an inter-Spike bivalent neutralizing antibody against SARS-CoV-2 variants. Iscience (2022)

Release Date

2022-06-15

Peptides

Spike glycoprotein: ABC
Angiotensin-converting enzyme 2: DE

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

Spike glycoprotein

Angiotensin-converting enzyme 2

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