SMTL ID : 8khc.1

SARS-CoV-2 Omicron spike in complex with 5817 Fab

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-2-2-mer

Ligands

2 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: 4 residues within 4Å: Chain A: N.691, L.896, Q.900, Q.1045 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:Q.900 NAG-NAG.2: 3 residues within 4Å: Chain B: N.691, L.896, Q.1045 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:L.896

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

NAG.3: 1 residues within 4Å: Chain A: N.631 Ligand excluded by PLIP NAG.4: 2 residues within 4Å: Chain A: N.308, Q.554 Ligand excluded by PLIP NAG.5: 3 residues within 4Å: Chain A: N.208 Chain C: K.436, E.439 Ligand excluded by PLIP NAG.6: 1 residues within 4Å: Chain A: N.577 Ligand excluded by PLIP NAG.7: 2 residues within 4Å: Chain A: E.1046, N.1048 Ligand excluded by PLIP NAG.8: 1 residues within 4Å: Chain A: N.1108 Ligand excluded by PLIP NAG.9: 4 residues within 4Å: Chain A: N.1072, T.1074, H.1075, F.1077 Ligand excluded by PLIP NAG.10: 1 residues within 4Å: Chain A: N.139 Ligand excluded by PLIP NAG.11: 3 residues within 4Å: Chain A: N.590, T.592, Q.618 Ligand excluded by PLIP NAG.12: 2 residues within 4Å: Chain A: N.683 Chain B: Y.770 Ligand excluded by PLIP NAG.13: 3 residues within 4Å: Chain A: N.775, S.777, Q.778 Ligand excluded by PLIP NAG.14: 2 residues within 4Å: Chain A: N.254, N.256 Ligand excluded by PLIP NAG.15: 3 residues within 4Å: Chain B: A.680, E.1046, N.1048 Ligand excluded by PLIP NAG.16: 3 residues within 4Å: Chain B: T.82, N.208, T.210 Ligand excluded by PLIP NAG.17: 2 residues within 4Å: Chain B: N.254, N.256 Ligand excluded by PLIP NAG.18: 3 residues within 4Å: Chain B: N.1072, G.1073, F.1077 Ligand excluded by PLIP NAG.19: 2 residues within 4Å: Chain B: N.775, N.902 Ligand excluded by PLIP NAG.20: 3 residues within 4Å: Chain B: N.683, I.1104 Chain C: Y.770 Ligand excluded by PLIP NAG.21: 3 residues within 4Å: Chain B: Y.629, V.630, N.631 Ligand excluded by PLIP NAG.22: 2 residues within 4Å: Chain B: N.590, Q.618 Ligand excluded by PLIP NAG.23: 2 residues within 4Å: Chain B: N.577, T.578 Ligand excluded by PLIP NAG.24: 3 residues within 4Å: Chain B: N.308, P.553, Q.554 Ligand excluded by PLIP NAG.25: 3 residues within 4Å: Chain B: S.86, E.106, N.139 Ligand excluded by PLIP NAG.26: 1 residues within 4Å: Chain B: N.1108 Ligand excluded by PLIP NAG.27: 1 residues within 4Å: Chain C: N.577 Ligand excluded by PLIP NAG.28: 1 residues within 4Å: Chain C: N.256 Ligand excluded by PLIP NAG.29: 2 residues within 4Å: Chain C: Y.629, N.631 Ligand excluded by PLIP NAG.30: 4 residues within 4Å: Chain C: N.305, P.553, Q.554, L.556 Ligand excluded by PLIP NAG.31: 1 residues within 4Å: Chain C: N.1108 Ligand excluded by PLIP NAG.32: 3 residues within 4Å: Chain C: T.82, N.208, T.210 Ligand excluded by PLIP NAG.33: 2 residues within 4Å: Chain C: N.683, I.1104 Ligand excluded by PLIP NAG.34: 4 residues within 4Å: Chain C: K.87, E.106, N.138, N.139 Ligand excluded by PLIP NAG.35: 3 residues within 4Å: Chain C: N.1072, H.1075, F.1077 Ligand excluded by PLIP NAG.36: 3 residues within 4Å: Chain C: N.775, S.777, Q.778 Ligand excluded by PLIP NAG.37: 2 residues within 4Å: Chain C: A.680, N.1048 Ligand excluded by PLIP NAG.38: 1 residues within 4Å: Chain C: N.590 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, Y. et al., Identification of a broad sarbecovirus neutralizing antibody targeting a conserved epitope on the receptor-binding domain. Cell Rep (2024)

Release Date

2024-04-17

Peptides

Spike glycoprotein: ABC
Heavy chain of 5817 Fab: DF
Light chain of 5817 Fab: EG

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
F

F
H

E
G

G
J

Spike glycoprotein

Heavy chain of 5817 Fab

Light chain of 5817 Fab

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