SMTL ID : 7tca.1

Cryo-EM structure of SARS-CoV-2 Omicron spike in complex with antibody A19-46.1

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-2-2-mer

Ligands

14 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.701, L.906 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.906 NAG-NAG.2: 3 residues within 4Å: Chain A: N.785, S.787, Q.788 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 4 residues within 4Å: Chain A: N.1082, T.1084, H.1085, F.1087 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 1 residues within 4Å: Chain A: N.1118 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 3 residues within 4Å: Chain B: N.701, L.906, Q.1055 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:L.906 NAG-NAG.6: 4 residues within 4Å: Chain B: N.1082, T.1084, H.1085, F.1087 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 2 residues within 4Å: Chain B: I.1116, N.1118 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 4 residues within 4Å: Chain B: N.315, P.563, Q.564, L.566 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 3 residues within 4Å: Chain B: N.785, S.787, Q.788 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 4 residues within 4Å: Chain C: T.700, N.701, L.906, Q.1055 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:L.906 NAG-NAG.11: 2 residues within 4Å: Chain C: N.1082, H.1085 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 2 residues within 4Å: Chain C: I.1116, N.1118 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 4 residues within 4Å: Chain C: N.315, T.317, P.563, Q.564 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 3 residues within 4Å: Chain C: N.785, S.787, Q.788 No protein-ligand interaction detected (PLIP)

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

NAG.15: 4 residues within 4Å: Chain A: N.264, E.265, N.266 Chain C: K.542 Ligand excluded by PLIP NAG.16: 2 residues within 4Å: Chain A: N.693 Chain B: Y.780 Ligand excluded by PLIP NAG.17: 4 residues within 4Å: Chain A: A.690, E.1056, N.1058 Chain B: Q.879 Ligand excluded by PLIP NAG.18: 1 residues within 4Å: Chain A: N.48 Ligand excluded by PLIP NAG.19: 2 residues within 4Å: Chain A: N.315, Q.564 Ligand excluded by PLIP NAG.20: 3 residues within 4Å: Chain A: D.323, N.327, L.355 Ligand excluded by PLIP NAG.21: 4 residues within 4Å: Chain A: N.600, T.602, Q.628 Chain B: Q.820 Ligand excluded by PLIP NAG.22: 1 residues within 4Å: Chain A: N.641 Ligand excluded by PLIP NAG.23: 2 residues within 4Å: Chain A: E.293, N.587 Ligand excluded by PLIP NAG.24: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP NAG.25: 3 residues within 4Å: Chain B: N.693 Chain C: I.778, Y.780 Ligand excluded by PLIP NAG.26: 3 residues within 4Å: Chain B: A.690, E.1056, N.1058 Ligand excluded by PLIP NAG.27: 3 residues within 4Å: Chain B: Y.15, N.48, P.615 Ligand excluded by PLIP NAG.28: 1 residues within 4Å: Chain B: N.641 Ligand excluded by PLIP NAG.29: 4 residues within 4Å: Chain B: N.600, T.602, E.603 Chain C: Q.820 Ligand excluded by PLIP NAG.30: 2 residues within 4Å: Chain B: T.586, N.587 Ligand excluded by PLIP NAG.31: 4 residues within 4Å: Chain A: K.542 Chain B: N.264, E.265, N.266 Ligand excluded by PLIP NAG.32: 2 residues within 4Å: Chain B: T.93, N.218 Ligand excluded by PLIP NAG.33: 6 residues within 4Å: Chain B: N.107, T.109, N.110, V.112, L.126, E.136 Ligand excluded by PLIP NAG.34: 2 residues within 4Å: Chain A: Y.780 Chain C: N.693 Ligand excluded by PLIP NAG.35: 4 residues within 4Å: Chain C: A.690, E.1056, K.1057, N.1058 Ligand excluded by PLIP NAG.36: 3 residues within 4Å: Chain C: Y.15, N.17, N.48 Ligand excluded by PLIP NAG.37: 1 residues within 4Å: Chain C: N.641 Ligand excluded by PLIP NAG.38: 1 residues within 4Å: Chain C: N.600 Ligand excluded by PLIP NAG.39: 1 residues within 4Å: Chain C: N.587 Ligand excluded by PLIP NAG.40: 3 residues within 4Å: Chain B: K.542 Chain C: E.265, N.266 Ligand excluded by PLIP NAG.41: 3 residues within 4Å: Chain C: T.93, N.218, T.220 Ligand excluded by PLIP NAG.42: 3 residues within 4Å: Chain C: N.107, T.109, N.110 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhou, T. et al., Structural basis for potent antibody neutralization of SARS-CoV-2 variants including B.1.1.529. Science (2022)

Release Date

2022-03-30

Peptides

Spike glycoprotein: ABC
Heavy chain of antibody A19-46.1: DF
Light chain of antibody A19-46.1: EG

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

F
H

E
E

G
L

Spike glycoprotein

Heavy chain of antibody A19-46.1

Light chain of antibody A19-46.1

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