SMTL ID : 7zrc.1

OMI-38 FAB IN COMPLEX WITH SARS-COV-2 BETA SPIKE

Coordinates

PDB Format

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.798, S.800, Q.801 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 4 residues within 4Å: Chain A: N.714, L.919, Q.923, Q.1068 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.919 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: 4 residues within 4Å: Chain B: N.714, L.919, Q.923, 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: 3 residues within 4Å: Chain B: N.1095, H.1098, F.1100 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 1 residues within 4Å: Chain B: N.1131 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 4 residues within 4Å: Chain C: N.714, L.919, Q.923, Q.1068 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 2 residues within 4Å: Chain C: N.798, S.800 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: 1 residues within 4Å: Chain C: N.1131 No protein-ligand interaction detected (PLIP)

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

NAG.13: 2 residues within 4Å: Chain A: N.277, N.279 Ligand excluded by PLIP NAG.14: 3 residues within 4Å: Chain A: N.328, Q.577, T.578 Ligand excluded by PLIP NAG.15: 2 residues within 4Å: Chain A: N.613, Q.641 Ligand excluded by PLIP NAG.16: 2 residues within 4Å: Chain A: H.652, N.654 Ligand excluded by PLIP NAG.17: 3 residues within 4Å: Chain A: N.706, G.1128 Chain B: D.793 Ligand excluded by PLIP NAG.18: 2 residues within 4Å: Chain A: E.1069, N.1071 Ligand excluded by PLIP NAG.19: 4 residues within 4Å: Chain A: S.112, E.132, N.164, N.165 Ligand excluded by PLIP NAG.20: 3 residues within 4Å: Chain A: N.340, L.365, S.368 Ligand excluded by PLIP NAG.21: 2 residues within 4Å: Chain A: Y.28, N.61 Ligand excluded by PLIP NAG.22: 4 residues within 4Å: Chain B: Y.28, T.29, N.30, N.61 Ligand excluded by PLIP NAG.23: 1 residues within 4Å: Chain B: N.279 Ligand excluded by PLIP NAG.24: 1 residues within 4Å: Chain B: N.600 Ligand excluded by PLIP NAG.25: 1 residues within 4Å: Chain B: N.613 Ligand excluded by PLIP NAG.26: 2 residues within 4Å: Chain B: H.652, N.654 Ligand excluded by PLIP NAG.27: 3 residues within 4Å: Chain B: N.706, G.1128 Chain C: D.793 Ligand excluded by PLIP NAG.28: 3 residues within 4Å: Chain B: A.703, E.1069, N.1071 Ligand excluded by PLIP NAG.29: 3 residues within 4Å: Chain B: N.328, P.576, Q.577 Ligand excluded by PLIP NAG.30: 2 residues within 4Å: Chain B: N.340, S.368 Ligand excluded by PLIP NAG.31: 2 residues within 4Å: Chain C: Y.28, N.61 Ligand excluded by PLIP NAG.32: 2 residues within 4Å: Chain B: K.555 Chain C: N.279 Ligand excluded by PLIP NAG.33: 4 residues within 4Å: Chain C: N.328, P.576, Q.577, L.579 Ligand excluded by PLIP NAG.34: 3 residues within 4Å: Chain C: K.307, N.600, T.601 Ligand excluded by PLIP NAG.35: 3 residues within 4Å: Chain C: N.613, T.615, Q.641 Ligand excluded by PLIP NAG.36: 2 residues within 4Å: Chain C: H.652, N.654 Ligand excluded by PLIP NAG.37: 3 residues within 4Å: Chain A: D.793 Chain C: N.706, G.1128 Ligand excluded by PLIP NAG.38: 3 residues within 4Å: Chain C: A.703, E.1069, N.1071 Ligand excluded by PLIP NAG.39: 4 residues within 4Å: Chain C: Q.115, E.132, N.165, T.167 Ligand excluded by PLIP NAG.40: 6 residues within 4Å: Chain C: F.335, 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-38 Fab Heavy Chain: DFH
Omi-38 Fab Light Chain: EGI

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
C

C
A

D
H

F
F

H
J

E
L

G
G

I
K

Spike glycoprotein,Fibritin

Omi-38 Fab Heavy Chain

Omi-38 Fab Light Chain

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