SMTL ID : 8dzi.1

Structure of SARS-CoV-2 Omicron BA.1.1.529 Spike trimer with one RBD down in complex with the Fab fragment of human neutralizing antibody MB.02

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-mer

Ligands

20 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: 3 residues within 4Å: Chain A: N.1095, T.1097, H.1098 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 2 residues within 4Å: Chain A: I.1129, N.1131 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 3 residues within 4Å: Chain A: N.706 Chain G: I.791, Y.793 1 PLIP interactions: 1 interactions with chain G Hydrophobic interactions: G:I.791 NAG-NAG.4: 5 residues within 4Å: Chain A: N.714, F.715, L.919, Q.923, Q.1068 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 3 residues within 4Å: Chain A: N.798, S.800, Q.801 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 2 residues within 4Å: Chain A: A.703, N.1071 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:A.703 NAG-NAG.7: 2 residues within 4Å: Chain A: E.278, N.279 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 4 residues within 4Å: Chain D: N.1095, T.1097, H.1098, F.1100 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 5 residues within 4Å: Chain A: I.791, Y.793 Chain D: Y.704, S.705, N.706 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:I.791 NAG-NAG.10: 3 residues within 4Å: Chain D: N.714, L.919, Q.1068 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 3 residues within 4Å: Chain D: N.798, S.800, Q.801 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 3 residues within 4Å: Chain A: Q.892 Chain D: A.703, N.1071 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 3 residues within 4Å: Chain D: E.278, N.279 Chain G: K.555 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 6 residues within 4Å: Chain G: N.120, A.121, N.123, V.125, E.151, Y.155 1 PLIP interactions: 1 interactions with chain G Hydrophobic interactions: G:V.125 NAG-NAG.15: 3 residues within 4Å: Chain A: K.555 Chain G: E.278, N.279 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 3 residues within 4Å: Chain D: I.791, Y.793 Chain G: N.706 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:Y.793 NAG-NAG.17: 1 residues within 4Å: Chain G: N.1131 No protein-ligand interaction detected (PLIP) NAG-NAG.18: 4 residues within 4Å: Chain G: N.1095, T.1097, H.1098, F.1100 No protein-ligand interaction detected (PLIP) NAG-NAG.19: 3 residues within 4Å: Chain G: T.713, N.714, L.919 No protein-ligand interaction detected (PLIP) NAG-NAG.20: 3 residues within 4Å: Chain G: N.798, S.800, Q.801 No protein-ligand interaction detected (PLIP)

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

NAG.21: 2 residues within 4Å: Chain A: T.304, N.600 Ligand excluded by PLIP NAG.22: 3 residues within 4Å: Chain A: Y.28, N.30, N.61 Ligand excluded by PLIP NAG.23: 5 residues within 4Å: Chain A: N.613, T.615, Q.641 Chain G: Y.834, G.835 Ligand excluded by PLIP NAG.24: 1 residues within 4Å: Chain A: N.654 Ligand excluded by PLIP NAG.25: 4 residues within 4Å: Chain A: T.106, T.107, T.233, R.234 Ligand excluded by PLIP NAG.26: 2 residues within 4Å: Chain D: N.600, T.601 Ligand excluded by PLIP NAG.27: 2 residues within 4Å: Chain D: Y.28, N.61 Ligand excluded by PLIP NAG.28: 4 residues within 4Å: Chain A: K.832, Q.833 Chain D: N.613, Q.641 Ligand excluded by PLIP NAG.29: 1 residues within 4Å: Chain D: N.654 Ligand excluded by PLIP NAG.30: 3 residues within 4Å: Chain D: I.1129, N.1131 Ligands: NAG.31 Ligand excluded by PLIP NAG.31: 1 residues within 4Å: Ligands: NAG.30 Ligand excluded by PLIP NAG.32: 4 residues within 4Å: Chain D: T.106, T.107, N.231, T.233 Ligand excluded by PLIP NAG.33: 5 residues within 4Å: Chain D: D.336, N.340, V.364, L.368 Ligands: NAG.34 Ligand excluded by PLIP NAG.34: 3 residues within 4Å: Chain D: N.367, L.368 Ligands: NAG.33 Ligand excluded by PLIP NAG.35: 3 residues within 4Å: Chain G: G.229, I.230, N.231 Ligand excluded by PLIP NAG.36: 3 residues within 4Å: Chain G: Y.28, N.30, N.61 Ligand excluded by PLIP NAG.37: 3 residues within 4Å: Chain G: N.328, P.576, Q.577 Ligand excluded by PLIP NAG.38: 4 residues within 4Å: Chain D: Q.833 Chain G: N.613, E.616, Q.641 Ligand excluded by PLIP NAG.39: 2 residues within 4Å: Chain G: Y.652, N.654 Ligand excluded by PLIP NAG.40: 1 residues within 4Å: Chain G: N.1071 Ligand excluded by PLIP NAG.41: 4 residues within 4Å: Chain G: D.336, N.340, L.368, A.369 Ligand excluded by PLIP NAG.42: 4 residues within 4Å: Chain G: E.130, N.160, C.161, T.162 Ligand excluded by PLIP NAG.43: 5 residues within 4Å: Chain G: C.134, N.135, D.136, F.138, R.153 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ren, P. et al., Function and Cryo-EM structures of broadly potent bispecific antibodies against multiple SARS-CoV-2 Omicron sublineages. Signal Transduct Target Ther (2023)

Release Date

2022-08-31

Peptides

Spike glycoprotein: ADG
antibody MB.02 heavy chain: BEI
antibody MB.02 light chain: CFH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

D
A

G
E

B
H

E
B

I
G

C
L

F
D

H
F

Spike glycoprotein

antibody MB.02 heavy chain

antibody MB.02 light chain

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