SMTL ID : 7yc5.1

Cryo-EM structure of SARS-CoV-2 spike in complex with K202.B bispecific antibody

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-mer

Ligands

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

NAG.1: 4 residues within 4Å: Chain A: F.338, G.339, F.342, N.343 Ligand excluded by PLIP NAG.2: 2 residues within 4Å: Chain A: Q.115, N.165 Ligand excluded by PLIP NAG.3: 4 residues within 4Å: Chain A: Y.28, T.29, N.30, N.61 Ligand excluded by PLIP NAG.4: 3 residues within 4Å: Chain A: N.280, E.281, N.282 Ligand excluded by PLIP NAG.5: 4 residues within 4Å: Chain A: N.331, Q.580, T.581, L.582 Ligand excluded by PLIP NAG.6: 3 residues within 4Å: Chain A: N.709, N.710, G.1131 Ligand excluded by PLIP NAG.7: 3 residues within 4Å: Chain A: K.795, N.801, S.803 Ligand excluded by PLIP NAG.8: 6 residues within 4Å: Chain A: A.706, A.713, E.1072, N.1074 Chain B: A.893, Q.895 Ligand excluded by PLIP NAG.9: 5 residues within 4Å: Chain A: N.1098, G.1099, T.1100, H.1101, F.1103 Ligand excluded by PLIP NAG.10: 3 residues within 4Å: Chain A: I.1132, V.1133, N.1134 Ligand excluded by PLIP NAG.11: 2 residues within 4Å: Chain A: N.616, Q.644 Ligand excluded by PLIP NAG.12: 4 residues within 4Å: Chain B: F.338, G.339, F.342, N.343 Ligand excluded by PLIP NAG.13: 2 residues within 4Å: Chain B: Q.115, N.165 Ligand excluded by PLIP NAG.14: 4 residues within 4Å: Chain B: Y.28, T.29, N.30, N.61 Ligand excluded by PLIP NAG.15: 2 residues within 4Å: Chain B: N.280, N.282 Ligand excluded by PLIP NAG.16: 3 residues within 4Å: Chain B: N.331, Q.580, L.582 Ligand excluded by PLIP NAG.17: 2 residues within 4Å: Chain B: N.709, G.1131 Ligand excluded by PLIP NAG.18: 1 residues within 4Å: Chain B: N.801 Ligand excluded by PLIP NAG.19: 4 residues within 4Å: Chain B: A.706, S.711, N.1074 Chain C: Q.895 Ligand excluded by PLIP NAG.20: 4 residues within 4Å: Chain B: N.1098, T.1100, H.1101, F.1103 Ligand excluded by PLIP NAG.21: 2 residues within 4Å: Chain B: V.1133, N.1134 Ligand excluded by PLIP NAG.22: 1 residues within 4Å: Chain B: N.616 Ligand excluded by PLIP NAG.23: 4 residues within 4Å: Chain C: F.338, G.339, F.342, N.343 Ligand excluded by PLIP NAG.24: 6 residues within 4Å: Chain B: R.357, Y.396 Chain C: Q.115, N.165, C.166, T.167 Ligand excluded by PLIP NAG.25: 3 residues within 4Å: Chain C: N.280, E.281, N.282 Ligand excluded by PLIP NAG.26: 2 residues within 4Å: Chain C: N.331, Q.580 Ligand excluded by PLIP NAG.27: 3 residues within 4Å: Chain C: N.709, N.710, G.1131 Ligand excluded by PLIP NAG.28: 2 residues within 4Å: Chain C: N.801, S.803 Ligand excluded by PLIP NAG.29: 2 residues within 4Å: Chain C: A.706, N.1074 Ligand excluded by PLIP NAG.30: 5 residues within 4Å: Chain C: N.1098, G.1099, T.1100, H.1101, F.1103 Ligand excluded by PLIP NAG.31: 3 residues within 4Å: Chain C: I.1132, V.1133, N.1134 Ligand excluded by PLIP NAG.32: 2 residues within 4Å: Chain C: N.616, Q.644 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kim, J.W. et al., Novel bispecific human antibody platform specifically targeting a fully open spike conformation potently neutralizes multiple SARS-CoV-2 variants. Antiviral Res. (2023)

Release Date

2023-07-05

Peptides

Spike glycoprotein: ABC
Bispecific anitybody (scFv and light chain of the antibody): DEF
Heavy chain from K202.B antibody: GHI

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

I
I

Spike glycoprotein

Bispecific anitybody (scFv and light chain of the antibody)

Heavy chain from K202.B antibody

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