SMTL ID : 8dzh.1

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

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-mer

Ligands

27 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, N.340, V.364, N.367, L.368 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 3 residues within 4Å: Chain A: N.798, S.800, Q.801 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 3 residues within 4Å: Chain A: N.714, L.919, Q.1068 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 3 residues within 4Å: Chain A: N.706 Chain B: I.791, Y.793 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 1 residues within 4Å: Chain A: N.1131 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 4 residues within 4Å: Chain A: N.1095, T.1097, H.1098, F.1100 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 3 residues within 4Å: Chain A: E.278, N.279 Chain C: K.555 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 3 residues within 4Å: Chain B: S.701, A.703, N.1071 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:A.703 NAG-NAG.9: 5 residues within 4Å: Chain B: D.336, N.340, V.364, N.367, L.368 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:V.364 NAG-NAG.10: 7 residues within 4Å: Chain B: N.120, A.121, N.123, V.125, M.148, E.151, Y.155 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:V.125 Hydrogen bonds: B:N.123 NAG-NAG.11: 5 residues within 4Å: Chain B: T.19, T.20, C.134, N.135, R.153 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.135 NAG-NAG.12: 3 residues within 4Å: Chain A: K.555 Chain B: E.278, N.279 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 3 residues within 4Å: Chain B: N.706 Chain C: I.791, Y.793 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:Y.793 NAG-NAG.14: 1 residues within 4Å: Chain B: N.1131 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 4 residues within 4Å: Chain B: N.1095, T.1097, H.1098, F.1100 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 3 residues within 4Å: Chain B: N.714, L.919, Q.1068 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:L.919 NAG-NAG.17: 3 residues within 4Å: Chain B: N.798, S.800, Q.801 No protein-ligand interaction detected (PLIP) NAG-NAG.18: 3 residues within 4Å: Chain C: N.328, Q.577, T.578 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:T.578 NAG-NAG.19: 4 residues within 4Å: Chain C: N.1095, T.1097, H.1098, F.1100 No protein-ligand interaction detected (PLIP) NAG-NAG.20: 1 residues within 4Å: Chain C: N.1131 No protein-ligand interaction detected (PLIP) NAG-NAG.21: 3 residues within 4Å: Chain A: I.791, Y.793 Chain C: N.706 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:I.791 NAG-NAG.22: 5 residues within 4Å: Chain C: N.714, T.716, L.919, Q.923, Q.1068 No protein-ligand interaction detected (PLIP) NAG-NAG.23: 3 residues within 4Å: Chain C: N.798, S.800, Q.801 No protein-ligand interaction detected (PLIP) NAG-NAG.24: 2 residues within 4Å: Chain C: A.703, N.1071 No protein-ligand interaction detected (PLIP) NAG-NAG.25: 3 residues within 4Å: Chain B: K.555 Chain C: N.277, N.279 No protein-ligand interaction detected (PLIP) NAG-NAG.26: 3 residues within 4Å: Chain C: T.106, N.231, T.233 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:T.106, C:T.233 NAG-NAG.27: 6 residues within 4Å: Chain C: D.336, N.340, V.364, N.367, L.368, F.371 No protein-ligand interaction detected (PLIP)

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

NAG.28: 6 residues within 4Å: Chain A: N.613, E.616, Q.641 Chain B: K.832, Y.834, D.836 Ligand excluded by PLIP NAG.29: 2 residues within 4Å: Chain A: N.328, Q.577 Ligand excluded by PLIP NAG.30: 2 residues within 4Å: Chain A: Y.652, N.654 Ligand excluded by PLIP NAG.31: 2 residues within 4Å: Chain A: E.1069, N.1071 Ligand excluded by PLIP NAG.32: 2 residues within 4Å: Chain A: Y.28, N.61 Ligand excluded by PLIP NAG.33: 6 residues within 4Å: Chain A: N.120, A.121, T.122, N.123, V.125, E.151 Ligand excluded by PLIP NAG.34: 2 residues within 4Å: Chain A: T.106, N.231 Ligand excluded by PLIP NAG.35: 3 residues within 4Å: Chain B: T.106, N.231, T.233 Ligand excluded by PLIP NAG.36: 2 residues within 4Å: Chain B: Y.28, N.61 Ligand excluded by PLIP NAG.37: 3 residues within 4Å: Chain B: N.328, P.576, Q.577 Ligand excluded by PLIP NAG.38: 3 residues within 4Å: Chain B: N.613, E.616 Chain C: Q.833 Ligand excluded by PLIP NAG.39: 2 residues within 4Å: Chain B: Y.652, N.654 Ligand excluded by PLIP NAG.40: 1 residues within 4Å: Chain B: N.160 Ligand excluded by PLIP NAG.41: 1 residues within 4Å: Chain C: N.600 Ligand excluded by PLIP NAG.42: 2 residues within 4Å: Chain C: Y.28, N.61 Ligand excluded by PLIP NAG.43: 3 residues within 4Å: Chain A: Y.834 Chain C: N.613, T.615 Ligand excluded by PLIP NAG.44: 2 residues within 4Å: Chain C: Y.652, N.654 Ligand excluded by PLIP NAG.45: 2 residues within 4Å: Chain C: E.130, N.160 Ligand excluded by PLIP NAG.46: 3 residues within 4Å: Chain C: N.120, N.123, V.125 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: ABC
antibody MB.02 heavy chain: DFH
antibody MB.02 light chain: EGI

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
A

C
C

D
E

F
H

H
I

E
D

G
L

I
J

Spike glycoprotein

antibody MB.02 heavy chain

antibody MB.02 light chain

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