SMTL ID : 7wt7.1

SARS-CoV-2 Omicron variant spike in complex with Fab 9A8 (State 1)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-1-1-mer

Ligands

1 x NAG- NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA.1: 4 residues within 4Å: Chain A: N.1095, T.1097, H.1098, F.1100 No protein-ligand interaction detected (PLIP)

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.2: 1 residues within 4Å: Chain A: N.1131 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 3 residues within 4Å: Chain C: N.714, T.716, L.919 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 3 residues within 4Å: Chain C: N.798, S.800, Q.801 No protein-ligand interaction detected (PLIP)

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

NAG.5: 4 residues within 4Å: Chain A: K.142, N.143, S.251, S.252 Ligand excluded by PLIP NAG.6: 4 residues within 4Å: Chain A: C.15, V.16, N.17, N.135 Ligand excluded by PLIP NAG.7: 4 residues within 4Å: Chain A: D.336, N.340, V.364, L.368 Ligand excluded by PLIP NAG.8: 2 residues within 4Å: Chain A: Y.28, N.61 Ligand excluded by PLIP NAG.9: 5 residues within 4Å: Chain A: T.106, N.231 Chain B: R.454, S.456, E.462 Ligand excluded by PLIP NAG.10: 1 residues within 4Å: Chain A: N.600 Ligand excluded by PLIP NAG.11: 1 residues within 4Å: Chain A: N.654 Ligand excluded by PLIP NAG.12: 2 residues within 4Å: Chain A: N.613, Q.641 Ligand excluded by PLIP NAG.13: 4 residues within 4Å: Chain A: N.714, F.715, Q.923, Q.1068 Ligand excluded by PLIP NAG.14: 1 residues within 4Å: Chain A: N.1071 Ligand excluded by PLIP NAG.15: 2 residues within 4Å: Chain A: N.798, S.800 Ligand excluded by PLIP NAG.16: 3 residues within 4Å: Chain A: N.706 Chain C: I.791, Y.793 Ligand excluded by PLIP NAG.17: 1 residues within 4Å: Chain B: N.1071 Ligand excluded by PLIP NAG.18: 1 residues within 4Å: Chain B: N.714 Ligand excluded by PLIP NAG.19: 3 residues within 4Å: Chain B: K.792, N.798, S.800 Ligand excluded by PLIP NAG.20: 3 residues within 4Å: Chain A: I.791, Y.793 Chain B: N.706 Ligand excluded by PLIP NAG.21: 2 residues within 4Å: Chain B: N.1095, H.1098 Ligand excluded by PLIP NAG.22: 1 residues within 4Å: Chain B: N.1131 Ligand excluded by PLIP NAG.23: 4 residues within 4Å: Chain B: N.120, A.121, T.122, N.123 Ligand excluded by PLIP NAG.24: 2 residues within 4Å: Chain B: N.143, S.251 Ligand excluded by PLIP NAG.25: 3 residues within 4Å: Chain B: C.15, V.16, N.17 Ligand excluded by PLIP NAG.26: 4 residues within 4Å: Chain B: D.336, F.339, N.340, V.364 Ligand excluded by PLIP NAG.27: 2 residues within 4Å: Chain B: Y.28, N.61 Ligand excluded by PLIP NAG.28: 1 residues within 4Å: Chain B: N.231 Ligand excluded by PLIP NAG.29: 1 residues within 4Å: Chain B: N.600 Ligand excluded by PLIP NAG.30: 2 residues within 4Å: Chain B: N.328, Q.577 Ligand excluded by PLIP NAG.31: 2 residues within 4Å: Chain B: N.613, Q.641 Ligand excluded by PLIP NAG.32: 1 residues within 4Å: Chain C: N.328 Ligand excluded by PLIP NAG.33: 2 residues within 4Å: Chain C: D.336, N.340 Ligand excluded by PLIP NAG.34: 2 residues within 4Å: Chain C: E.306, N.600 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 B: Y.793 Chain C: N.706 Ligand excluded by PLIP NAG.37: 3 residues within 4Å: Chain C: N.120, A.121, F.152 Ligand excluded by PLIP NAG.38: 5 residues within 4Å: Chain C: K.142, N.143, N.144, S.146, M.148 Ligand excluded by PLIP NAG.39: 2 residues within 4Å: Chain C: N.17, N.135 Ligand excluded by PLIP NAG.40: 2 residues within 4Å: Chain C: Y.28, N.61 Ligand excluded by PLIP NAG.41: 6 residues within 4Å: Chain A: R.454, K.459, E.462 Chain C: T.106, N.231, T.233 Ligand excluded by PLIP NAG.42: 1 residues within 4Å: Chain C: N.654 Ligand excluded by PLIP NAG.43: 2 residues within 4Å: Chain C: S.708, N.1071 Ligand excluded by PLIP NAG.44: 4 residues within 4Å: Chain C: N.1095, T.1097, H.1098, F.1100 Ligand excluded by PLIP NAG.45: 1 residues within 4Å: Chain C: N.1131 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Liu, S. et al., A broader neutralizing antibody against all the current VOCs and VOIs targets unique epitope of SARS-CoV-2 RBD. Cell Discov (2022)

Release Date

2023-06-07

Peptides

Spike glycoprotein: ABC
Heavy chain of Fab 9A8: D
Light chain of Fab 9A8: E

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
H

E
D

Spike glycoprotein

Heavy chain of Fab 9A8

Light chain of Fab 9A8

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