SMTL ID : 7zr9.1

OMI-2 FAB IN COMPLEX WITH SARS-COV-2 BETA SPIKE GLYCOPROTEIN

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-mer

Ligands

12 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.714, Q.923, Q.1068 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: 4 residues within 4Å: Chain A: N.1095, T.1097, H.1098, F.1100 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 1 residues within 4Å: Chain A: N.1131 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 3 residues within 4Å: Chain B: N.714, L.919, Q.1068 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 3 residues within 4Å: Chain B: N.798, S.800, Q.801 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 4 residues within 4Å: Chain B: N.1095, T.1097, H.1098, F.1100 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 2 residues within 4Å: Chain B: I.1129, N.1131 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 3 residues within 4Å: Chain C: N.714, L.919, Q.923 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 3 residues within 4Å: Chain C: N.798, S.800, Q.801 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 4 residues within 4Å: Chain C: N.1095, T.1097, H.1098, F.1100 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 2 residues within 4Å: Chain C: I.1129, N.1131 No protein-ligand interaction detected (PLIP)

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

NAG.13: 2 residues within 4Å: Chain A: Y.28, N.61 Ligand excluded by PLIP NAG.14: 3 residues within 4Å: Chain A: N.277, N.279 Chain B: K.555 Ligand excluded by PLIP NAG.15: 2 residues within 4Å: Chain A: N.328, Q.577 Ligand excluded by PLIP NAG.16: 1 residues within 4Å: Chain A: N.600 Ligand excluded by PLIP NAG.17: 1 residues within 4Å: Chain A: N.613 Ligand excluded by PLIP NAG.18: 1 residues within 4Å: Chain A: N.654 Ligand excluded by PLIP NAG.19: 3 residues within 4Å: Chain A: N.706, N.707, G.1128 Ligand excluded by PLIP NAG.20: 3 residues within 4Å: Chain A: A.703, E.1069, N.1071 Ligand excluded by PLIP NAG.21: 2 residues within 4Å: Chain A: E.132, N.165 Ligand excluded by PLIP NAG.22: 5 residues within 4Å: Chain A: G.336, F.339, N.340, L.365, S.368 Ligand excluded by PLIP NAG.23: 2 residues within 4Å: Chain B: Y.28, N.61 Ligand excluded by PLIP NAG.24: 2 residues within 4Å: Chain B: E.278, N.279 Ligand excluded by PLIP NAG.25: 2 residues within 4Å: Chain B: N.328, Q.577 Ligand excluded by PLIP NAG.26: 1 residues within 4Å: Chain B: N.600 Ligand excluded by PLIP NAG.27: 1 residues within 4Å: Chain B: N.613 Ligand excluded by PLIP NAG.28: 2 residues within 4Å: Chain B: H.652, N.654 Ligand excluded by PLIP NAG.29: 3 residues within 4Å: Chain A: D.793 Chain B: N.706, G.1128 Ligand excluded by PLIP NAG.30: 3 residues within 4Å: Chain B: A.703, E.1069, N.1071 Ligand excluded by PLIP NAG.31: 2 residues within 4Å: Chain B: E.132, N.165 Ligand excluded by PLIP NAG.32: 4 residues within 4Å: Chain B: F.339, N.340, L.365, S.368 Ligand excluded by PLIP NAG.33: 2 residues within 4Å: Chain C: Y.28, N.61 Ligand excluded by PLIP NAG.34: 1 residues within 4Å: Chain C: N.279 Ligand excluded by PLIP NAG.35: 3 residues within 4Å: Chain C: N.328, T.330, Q.577 Ligand excluded by PLIP NAG.36: 1 residues within 4Å: Chain C: N.600 Ligand excluded by PLIP NAG.37: 1 residues within 4Å: Chain C: N.613 Ligand excluded by PLIP NAG.38: 1 residues within 4Å: Chain C: N.654 Ligand excluded by PLIP NAG.39: 3 residues within 4Å: Chain B: D.793 Chain C: N.706, G.1128 Ligand excluded by PLIP NAG.40: 3 residues within 4Å: Chain C: A.703, E.1069, N.1071 Ligand excluded by PLIP NAG.41: 2 residues within 4Å: Chain C: E.132, N.165 Ligand excluded by PLIP NAG.42: 5 residues within 4Å: Chain C: G.336, F.339, N.340, L.365, S.368 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nutalai, R. et al., Potent cross-reactive antibodies following Omicron breakthrough in vaccinees. Cell (2022)

Release Date

2022-06-01

Peptides

Spike glycoprotein,Fibritin: ABC
Omi-2 Fab heavy chain: DFH
Omi-2 Fab light chain: EGI

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
A

C
C

D
H

F
D

H
F

E
L

G
E

I
G

Spike glycoprotein,Fibritin

Omi-2 Fab heavy chain

Omi-2 Fab light chain

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