SMTL ID : 7wo5.1

SARS-CoV-2 Spike in complex with IgG 553-15 (S-553-15 trimer)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-mer

Ligands

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

NAG.1: 4 residues within 4Å: Chain A: K.113, E.132, N.164, N.165 Ligand excluded by PLIP NAG.2: 2 residues within 4Å: Chain A: N.331, Q.580 Ligand excluded by PLIP NAG.3: 3 residues within 4Å: Chain A: G.339, F.342, N.343 Ligand excluded by PLIP NAG.4: 3 residues within 4Å: Chain A: N.616, T.618, Q.644 Ligand excluded by PLIP NAG.5: 3 residues within 4Å: Chain A: N.709, I.1130, G.1131 Ligand excluded by PLIP NAG.6: 1 residues within 4Å: Chain A: N.717 Ligand excluded by PLIP NAG.7: 3 residues within 4Å: Chain A: A.706, N.1074, T.1076 Ligand excluded by PLIP NAG.8: 1 residues within 4Å: Chain A: N.1134 Ligand excluded by PLIP NAG.9: 2 residues within 4Å: Chain A: E.281, N.282 Ligand excluded by PLIP NAG.10: 2 residues within 4Å: Chain A: Y.28, N.61 Ligand excluded by PLIP NAG.11: 2 residues within 4Å: Chain A: N.801, S.803 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: 4 residues within 4Å: Chain A: C.15, V.16, N.17, N.137 Ligand excluded by PLIP NAG.14: 5 residues within 4Å: Chain A: N.122, T.124, N.125, V.127, E.154 Ligand excluded by PLIP NAG.15: 5 residues within 4Å: Chain A: Y.145, N.148, N.149, S.151, M.153 Ligand excluded by PLIP NAG.16: 1 residues within 4Å: Chain B: N.1134 Ligand excluded by PLIP NAG.17: 4 residues within 4Å: Chain B: N.1098, T.1100, H.1101, F.1103 Ligand excluded by PLIP NAG.18: 3 residues within 4Å: Chain B: N.801, S.803, Q.804 Ligand excluded by PLIP NAG.19: 3 residues within 4Å: Chain B: N.717, L.922, Q.1071 Ligand excluded by PLIP NAG.20: 3 residues within 4Å: Chain B: N.709, I.1130, G.1131 Ligand excluded by PLIP NAG.21: 3 residues within 4Å: Chain B: N.616, Q.644, T.645 Ligand excluded by PLIP NAG.22: 4 residues within 4Å: Chain B: F.338, G.339, F.342, N.343 Ligand excluded by PLIP NAG.23: 2 residues within 4Å: Chain B: N.331, Q.580 Ligand excluded by PLIP NAG.24: 2 residues within 4Å: Chain B: E.281, N.282 Ligand excluded by PLIP NAG.25: 3 residues within 4Å: Chain B: E.132, N.164, N.165 Ligand excluded by PLIP NAG.26: 3 residues within 4Å: Chain B: Y.28, T.29, N.61 Ligand excluded by PLIP NAG.27: 3 residues within 4Å: Chain B: C.15, N.17, N.137 Ligand excluded by PLIP NAG.28: 3 residues within 4Å: Chain B: H.146, N.149, S.151 Ligand excluded by PLIP NAG.29: 4 residues within 4Å: Chain B: N.122, A.123, T.124, N.125 Ligand excluded by PLIP NAG.30: 3 residues within 4Å: Chain B: A.706, N.1074 Chain C: Q.895 Ligand excluded by PLIP NAG.31: 3 residues within 4Å: Chain C: N.280, E.281, N.282 Ligand excluded by PLIP NAG.32: 3 residues within 4Å: Chain C: N.331, Q.580, T.581 Ligand excluded by PLIP NAG.33: 2 residues within 4Å: Chain C: N.343, V.367 Ligand excluded by PLIP NAG.34: 3 residues within 4Å: Chain C: N.616, T.618, Q.644 Ligand excluded by PLIP NAG.35: 2 residues within 4Å: Chain C: N.709, G.1131 Ligand excluded by PLIP NAG.36: 2 residues within 4Å: Chain C: N.717, L.922 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: 1 residues within 4Å: Chain C: N.1134 Ligand excluded by PLIP NAG.39: 3 residues within 4Å: Chain C: N.801, S.803, Q.804 Ligand excluded by PLIP NAG.40: 3 residues within 4Å: Chain C: N.1098, H.1101, F.1103 Ligand excluded by PLIP NAG.41: 3 residues within 4Å: Chain C: C.15, N.17, N.137 Ligand excluded by PLIP NAG.42: 4 residues within 4Å: Chain C: H.146, N.148, N.149, M.153 Ligand excluded by PLIP NAG.43: 2 residues within 4Å: Chain C: Y.28, N.61 Ligand excluded by PLIP NAG.44: 5 residues within 4Å: Chain C: N.122, A.123, T.124, V.127, E.154 Ligand excluded by PLIP NAG.45: 4 residues within 4Å: Chain C: Q.115, E.132, N.165, T.167 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
mAb15 VH: DFH
mAb15 VL: EGI

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

F
F

H
H

E
E

G
G

I
I

Spike glycoprotein

mAb15 VH

mAb15 VL

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