SMTL ID : 7wt8.1

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

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-2-2-mer

Ligands

16 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: 4 residues within 4Å: Chain A: N.277, E.278, N.279 Chain B: K.555 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 3 residues within 4Å: Chain A: R.325, N.328, Q.577 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 2 residues within 4Å: Chain A: N.714, Q.923 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 2 residues within 4Å: Chain A: N.798, S.800 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 4 residues within 4Å: Chain A: N.1095, T.1097, H.1098, F.1100 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 1 residues within 4Å: Chain A: N.1131 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 7 residues within 4Å: Chain B: F.335, D.336, F.339, N.340, V.364, N.367, L.368 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 5 residues within 4Å: Chain B: N.714, N.916, L.919, Q.923, Q.1068 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 3 residues within 4Å: Chain B: N.798, S.800, Q.801 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 3 residues within 4Å: Chain B: N.1095, H.1098, F.1100 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 1 residues within 4Å: Chain B: N.1131 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 3 residues within 4Å: Chain C: N.328, T.330, Q.577 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 2 residues within 4Å: Chain C: N.714, L.919 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 3 residues within 4Å: Chain C: N.798, S.800, Q.801 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 4 residues within 4Å: Chain C: N.1095, T.1097, H.1098, F.1100 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 1 residues within 4Å: Chain C: N.1131 No protein-ligand interaction detected (PLIP)

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

NAG.17: 3 residues within 4Å: Chain A: C.15, N.17, D.136 Ligand excluded by PLIP NAG.18: 4 residues within 4Å: Chain A: Y.28, T.29, N.30, N.61 Ligand excluded by PLIP NAG.19: 3 residues within 4Å: Chain A: E.130, N.160 Chain B: I.465 Ligand excluded by PLIP NAG.20: 4 residues within 4Å: Chain A: F.335, D.336, N.340, L.368 Ligand excluded by PLIP NAG.21: 1 residues within 4Å: Chain A: N.600 Ligand excluded by PLIP NAG.22: 2 residues within 4Å: Chain A: N.613, T.615 Ligand excluded by PLIP NAG.23: 2 residues within 4Å: Chain A: Y.652, N.654 Ligand excluded by PLIP NAG.24: 3 residues within 4Å: Chain A: Y.704, S.705, N.706 Ligand excluded by PLIP NAG.25: 1 residues within 4Å: Chain A: N.1071 Ligand excluded by PLIP NAG.26: 2 residues within 4Å: Chain B: C.15, N.17 Ligand excluded by PLIP NAG.27: 2 residues within 4Å: Chain B: Y.28, N.61 Ligand excluded by PLIP NAG.28: 6 residues within 4Å: Chain B: N.120, A.121, T.122, N.123, V.125, V.166 Ligand excluded by PLIP NAG.29: 2 residues within 4Å: Chain B: N.159, N.160 Ligand excluded by PLIP NAG.30: 11 residues within 4Å: Chain B: Y.38, F.43, N.277, E.278, N.279, G.280, T.281 Chain C: K.554, K.555, L.557, Q.560 Ligand excluded by PLIP NAG.31: 1 residues within 4Å: Chain B: N.328 Ligand excluded by PLIP NAG.32: 1 residues within 4Å: Chain B: N.600 Ligand excluded by PLIP NAG.33: 2 residues within 4Å: Chain B: N.613, Q.641 Ligand excluded by PLIP NAG.34: 1 residues within 4Å: Chain B: N.654 Ligand excluded by PLIP NAG.35: 2 residues within 4Å: Chain A: I.791 Chain B: N.706 Ligand excluded by PLIP NAG.36: 2 residues within 4Å: Chain A: Q.892 Chain B: N.1071 Ligand excluded by PLIP NAG.37: 3 residues within 4Å: Chain C: N.17, T.19, N.135 Ligand excluded by PLIP NAG.38: 2 residues within 4Å: Chain C: Y.28, N.61 Ligand excluded by PLIP NAG.39: 4 residues within 4Å: Chain C: N.120, A.121, N.123, V.125 Ligand excluded by PLIP NAG.40: 4 residues within 4Å: Chain C: Q.113, E.130, N.160, T.162 Ligand excluded by PLIP NAG.41: 2 residues within 4Å: Chain C: E.278, N.279 Ligand excluded by PLIP NAG.42: 3 residues within 4Å: Chain C: D.336, N.340, V.364 Ligand excluded by PLIP NAG.43: 3 residues within 4Å: Chain C: E.306, N.600, T.601 Ligand excluded by PLIP NAG.44: 2 residues within 4Å: Chain C: N.613, T.615 Ligand excluded by PLIP NAG.45: 2 residues within 4Å: Chain C: Y.652, N.654 Ligand excluded by PLIP NAG.46: 1 residues within 4Å: Chain C: N.706 Ligand excluded by PLIP NAG.47: 1 residues within 4Å: Chain C: N.1071 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
light chain of Fab 9A8: DF
Heavy chain of Fab 9A8: EG

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

F
I

E
H

G
J

Spike glycoprotein

light chain of Fab 9A8

Heavy chain of Fab 9A8

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