SMTL ID : 7tcc.1

Cryo-EM structure of SARS-CoV-2 Omicron spike in complex with antibodies A19-46.1 and B1-182.1

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-3-3-mer

Ligands

13 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: 1 residues within 4Å: Chain A: N.701 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 4 residues within 4Å: Chain A: N.1082, T.1084, H.1085, F.1087 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 1 residues within 4Å: Chain A: N.1118 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 3 residues within 4Å: Chain A: N.785, S.787, Q.788 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 2 residues within 4Å: Chain B: N.701, L.906 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 2 residues within 4Å: Chain B: N.1082, H.1085 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 1 residues within 4Å: Chain B: N.1118 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 3 residues within 4Å: Chain B: N.785, S.787, Q.788 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 3 residues within 4Å: Chain C: N.701, L.906, Q.1055 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 4 residues within 4Å: Chain C: N.1082, T.1084, H.1085, F.1087 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 1 residues within 4Å: Chain C: N.1118 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 5 residues within 4Å: Chain C: N.315, I.316, Q.564, T.565, L.566 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 3 residues within 4Å: Chain C: N.785, S.787, Q.788 No protein-ligand interaction detected (PLIP)

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

NAG.14: 3 residues within 4Å: Chain A: N.693 Chain B: I.778, Y.780 Ligand excluded by PLIP NAG.15: 2 residues within 4Å: Chain A: A.690, N.1058 Ligand excluded by PLIP NAG.16: 1 residues within 4Å: Chain A: N.641 Ligand excluded by PLIP NAG.17: 3 residues within 4Å: Chain A: N.600, T.602 Chain B: Q.820 Ligand excluded by PLIP NAG.18: 3 residues within 4Å: Chain A: E.265, N.266 Chain C: K.542 Ligand excluded by PLIP NAG.19: 4 residues within 4Å: Chain A: N.107, T.109, N.110, E.136 Ligand excluded by PLIP NAG.20: 1 residues within 4Å: Chain B: N.693 Ligand excluded by PLIP NAG.21: 3 residues within 4Å: Chain B: A.690, E.1056, N.1058 Ligand excluded by PLIP NAG.22: 4 residues within 4Å: Chain B: N.600, E.603, Q.628 Chain C: Q.820 Ligand excluded by PLIP NAG.23: 3 residues within 4Å: Chain B: N.264, E.265, N.266 Ligand excluded by PLIP NAG.24: 4 residues within 4Å: Chain B: N.315, P.563, Q.564, L.566 Ligand excluded by PLIP NAG.25: 2 residues within 4Å: Chain A: Y.780 Chain C: N.693 Ligand excluded by PLIP NAG.26: 5 residues within 4Å: Chain A: Q.820, D.823 Chain C: N.600, T.602, E.603 Ligand excluded by PLIP NAG.27: 3 residues within 4Å: Chain C: N.264, E.265, N.266 Ligand excluded by PLIP NAG.28: 4 residues within 4Å: Chain C: N.107, T.109, N.110, V.112 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: DHJ
Light chain of antibody A19-46.1: EIK
heavy chain of antibody B1-182.1: FLN
Light chain of antibody B1-182.1: GMO

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

H
H

J
M

E
E

I
L

K
N

F
J

L
O

N
F

G
K

M
P

O
G

Spike glycoprotein

Heavy chain of antibody A19-46.1

Light chain of antibody A19-46.1

heavy chain of antibody B1-182.1

Light chain of antibody B1-182.1

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