SMTL ID : 7woa.1

SARS-CoV-2 Spike in complex with IgG 553-60 (1-up trimer)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-2-2-mer

Ligands

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

NAG.1: 3 residues within 4Å: Chain A: T.29, N.30, N.61 Ligand excluded by PLIP NAG.2: 3 residues within 4Å: Chain A: A.163, N.164, N.165 Ligand excluded by PLIP NAG.3: 4 residues within 4Å: Chain A: T.108, N.234, T.236 Chain C: K.462 Ligand excluded by PLIP NAG.4: 1 residues within 4Å: Chain A: N.282 Ligand excluded by PLIP NAG.5: 2 residues within 4Å: Chain A: N.331, Q.580 Ligand excluded by PLIP NAG.6: 4 residues within 4Å: Chain A: F.338, G.339, N.343, S.373 Ligand excluded by PLIP NAG.7: 2 residues within 4Å: Chain A: N.616, Q.644 Ligand excluded by PLIP NAG.8: 1 residues within 4Å: Chain A: N.709 Ligand excluded by PLIP NAG.9: 4 residues within 4Å: Chain A: N.717, L.922, Q.926, Q.1071 Ligand excluded by PLIP NAG.10: 3 residues within 4Å: Chain A: N.801, S.803, Q.804 Ligand excluded by PLIP NAG.11: 4 residues within 4Å: Chain A: A.706, E.1072, K.1073, N.1074 Ligand excluded by PLIP NAG.12: 4 residues within 4Å: Chain A: N.1098, T.1100, H.1101, F.1103 Ligand excluded by PLIP NAG.13: 1 residues within 4Å: Chain A: N.1134 Ligand excluded by PLIP NAG.14: 2 residues within 4Å: Chain B: Y.28, N.61 Ligand excluded by PLIP NAG.15: 2 residues within 4Å: Chain B: N.164, N.165 Ligand excluded by PLIP NAG.16: 3 residues within 4Å: Chain B: T.108, N.234, T.236 Ligand excluded by PLIP NAG.17: 5 residues within 4Å: Chain A: N.556, K.557, K.558 Chain B: E.281, N.282 Ligand excluded by PLIP NAG.18: 2 residues within 4Å: Chain B: N.331, Q.580 Ligand excluded by PLIP NAG.19: 4 residues within 4Å: Chain B: F.338, F.342, N.343, L.368 Ligand excluded by PLIP NAG.20: 3 residues within 4Å: Chain B: N.616, T.618, Q.644 Ligand excluded by PLIP NAG.21: 3 residues within 4Å: Chain B: N.709, I.1130, G.1131 Ligand excluded by PLIP NAG.22: 4 residues within 4Å: Chain B: N.717, F.718, L.922, Q.926 Ligand excluded by PLIP NAG.23: 3 residues within 4Å: Chain B: N.801, S.803, Q.804 Ligand excluded by PLIP NAG.24: 4 residues within 4Å: Chain B: A.706, S.711, N.1074 Chain C: Q.895 Ligand excluded by PLIP NAG.25: 4 residues within 4Å: Chain B: N.1098, T.1100, H.1101, F.1103 Ligand excluded by PLIP NAG.26: 1 residues within 4Å: Chain B: N.1134 Ligand excluded by PLIP NAG.27: 2 residues within 4Å: Chain C: Y.28, N.61 Ligand excluded by PLIP NAG.28: 3 residues within 4Å: Chain C: Q.115, E.132, N.165 Ligand excluded by PLIP NAG.29: 3 residues within 4Å: Chain C: T.108, N.234, T.236 Ligand excluded by PLIP NAG.30: 3 residues within 4Å: Chain C: N.280, E.281, N.282 Ligand excluded by PLIP NAG.31: 3 residues within 4Å: Chain C: N.331, P.579, Q.580 Ligand excluded by PLIP NAG.32: 4 residues within 4Å: Chain C: F.338, G.339, F.342, N.343 Ligand excluded by PLIP NAG.33: 2 residues within 4Å: Chain C: N.616, Q.644 Ligand excluded by PLIP NAG.34: 3 residues within 4Å: Chain C: N.709, N.710, G.1131 Ligand excluded by PLIP NAG.35: 3 residues within 4Å: Chain C: N.717, L.922, Q.926 Ligand excluded by PLIP NAG.36: 3 residues within 4Å: Chain C: K.795, N.801, S.803 Ligand excluded by PLIP NAG.37: 4 residues within 4Å: Chain C: A.706, E.1072, K.1073, N.1074 Ligand excluded by PLIP NAG.38: 4 residues within 4Å: Chain C: N.1098, T.1100, H.1101, F.1103 Ligand excluded by PLIP NAG.39: 2 residues within 4Å: Chain C: I.1132, N.1134 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhan, W. et al., Structural Study of SARS-CoV-2 Antibodies Identifies a Broad-Spectrum Antibody That Neutralizes the Omicron Variant by Disassembling the Spike Trimer. J.Virol. (2022)

Release Date

2022-07-20

Peptides

Spike glycoprotein: ABC
mAb60 VH: DF
mAb60 VL: EG

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

C
E

D
D

F
F

E
B

G
G

Spike glycoprotein

mAb60 VH

mAb60 VL

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