SMTL ID : 7uz8.1

Structure of the SARS-CoV-2 Omicron BA.1 S 6P trimer in complex with the mouse antibody Fab fragment, M8a-31

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-mer

Ligands

3 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: 5 residues within 4Å: Chain A: D.336, F.339, N.340, V.364, L.368 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.336 NAG-NAG.2: 5 residues within 4Å: Chain B: D.336, F.339, N.340, V.364, L.368 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.336 NAG-NAG.3: 5 residues within 4Å: Chain C: D.336, F.339, N.340, V.364, L.368 No protein-ligand interaction detected (PLIP)

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

NAG.4: 4 residues within 4Å: Chain A: N.277, E.278, N.279, T.281 Ligand excluded by PLIP NAG.5: 2 residues within 4Å: Chain A: N.328, Q.577 Ligand excluded by PLIP NAG.6: 1 residues within 4Å: Chain A: N.613 Ligand excluded by PLIP NAG.7: 3 residues within 4Å: Chain A: N.703 Chain B: I.788, Y.790 Ligand excluded by PLIP NAG.8: 4 residues within 4Å: Chain A: N.711, L.916, Q.920, Q.1065 Ligand excluded by PLIP NAG.9: 3 residues within 4Å: Chain A: N.795, S.797, Q.798 Ligand excluded by PLIP NAG.10: 4 residues within 4Å: Chain A: A.700, E.1066, K.1067, N.1068 Ligand excluded by PLIP NAG.11: 4 residues within 4Å: Chain A: N.1092, T.1094, H.1095, F.1097 Ligand excluded by PLIP NAG.12: 2 residues within 4Å: Chain A: I.1126, N.1128 Ligand excluded by PLIP NAG.13: 4 residues within 4Å: Chain B: N.277, E.278, N.279, T.281 Ligand excluded by PLIP NAG.14: 3 residues within 4Å: Chain B: N.328, Q.577, L.579 Ligand excluded by PLIP NAG.15: 1 residues within 4Å: Chain B: N.613 Ligand excluded by PLIP NAG.16: 3 residues within 4Å: Chain B: N.703 Chain C: I.788, Y.790 Ligand excluded by PLIP NAG.17: 4 residues within 4Å: Chain B: N.711, L.916, Q.920, Q.1065 Ligand excluded by PLIP NAG.18: 2 residues within 4Å: Chain B: N.795, S.797 Ligand excluded by PLIP NAG.19: 4 residues within 4Å: Chain B: A.700, E.1066, K.1067, N.1068 Ligand excluded by PLIP NAG.20: 4 residues within 4Å: Chain B: N.1092, T.1094, H.1095, F.1097 Ligand excluded by PLIP NAG.21: 2 residues within 4Å: Chain B: I.1126, N.1128 Ligand excluded by PLIP NAG.22: 4 residues within 4Å: Chain C: N.277, E.278, N.279, T.281 Ligand excluded by PLIP NAG.23: 2 residues within 4Å: Chain C: N.328, Q.577 Ligand excluded by PLIP NAG.24: 1 residues within 4Å: Chain C: N.613 Ligand excluded by PLIP NAG.25: 3 residues within 4Å: Chain A: I.788, Y.790 Chain C: N.703 Ligand excluded by PLIP NAG.26: 3 residues within 4Å: Chain C: N.711, L.916, Q.1065 Ligand excluded by PLIP NAG.27: 2 residues within 4Å: Chain C: N.795, S.797 Ligand excluded by PLIP NAG.28: 4 residues within 4Å: Chain C: A.700, E.1066, K.1067, N.1068 Ligand excluded by PLIP NAG.29: 4 residues within 4Å: Chain C: N.1092, T.1094, H.1095, F.1097 Ligand excluded by PLIP NAG.30: 3 residues within 4Å: Chain C: I.1126, V.1127, N.1128 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fan, C. et al., Neutralizing monoclonal antibodies elicited by mosaic RBD nanoparticles bind conserved sarbecovirus epitopes. Immunity (2022)

Release Date

2022-12-07

Peptides

Spike glycoprotein: ABC
M8a-31 Fab heavy chain: DFH
M8a-31 Fab light chain: EGI

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
H

F
M

H
P

E
L

G
N

I
Q

Spike glycoprotein

M8a-31 Fab heavy chain

M8a-31 Fab light chain

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