SMTL ID : 8zbz.1

SARS-CoV-2 Omicron BA.2 spike trimer (6P) in complex with 3 D1F6 Fabs (1 RBD up)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-mer

Ligands

15 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.697, L.902, Q.906 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 4 residues within 4Å: Chain A: N.781, S.783, Q.784, Q.915 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 5 residues within 4Å: Chain A: S.684, V.685, A.686, E.1052, N.1054 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:A.686 NAG-NAG.5: 1 residues within 4Å: Chain A: N.1114 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 6 residues within 4Å: Chain B: V.104, N.106, T.108, N.109, V.111, V.155 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 3 residues within 4Å: Chain A: I.774, Y.776 Chain B: N.689 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 4 residues within 4Å: Chain B: N.697, L.902, Q.906, Q.1051 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:L.902 NAG-NAG.9: 2 residues within 4Å: Chain B: N.781, S.783 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 3 residues within 4Å: Chain A: Q.875 Chain B: A.686, N.1054 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 4 residues within 4Å: Chain B: N.1078, T.1080, H.1081, F.1083 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 1 residues within 4Å: Chain B: N.1114 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 2 residues within 4Å: Chain B: N.315, Q.564 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 2 residues within 4Å: Chain C: N.697, L.902 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 3 residues within 4Å: Chain C: N.781, S.783, Q.784 No protein-ligand interaction detected (PLIP) NAG-NAG.17: 2 residues within 4Å: Chain C: I.1112, N.1114 No protein-ligand interaction detected (PLIP)

2 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.4: 4 residues within 4Å: Chain A: N.1078, G.1079, H.1081, F.1083 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.16: 3 residues within 4Å: Chain C: N.1078, G.1079, F.1083 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:F.1083

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

NAG.18: 2 residues within 4Å: Chain A: N.266 Chain B: K.542 Ligand excluded by PLIP NAG.19: 2 residues within 4Å: Chain A: N.315, Q.564 Ligand excluded by PLIP NAG.20: 2 residues within 4Å: Chain A: N.587, T.588 Ligand excluded by PLIP NAG.21: 2 residues within 4Å: Chain A: N.600, T.602 Ligand excluded by PLIP NAG.22: 2 residues within 4Å: Chain A: Y.639, N.641 Ligand excluded by PLIP NAG.23: 3 residues within 4Å: Chain A: S.688, N.689 Chain C: Y.776 Ligand excluded by PLIP NAG.24: 3 residues within 4Å: Chain A: Y.12, N.45, T.47 Ligand excluded by PLIP NAG.25: 1 residues within 4Å: Chain A: N.218 Ligand excluded by PLIP NAG.26: 4 residues within 4Å: Chain B: Y.12, T.13, N.14, N.45 Ligand excluded by PLIP NAG.27: 2 residues within 4Å: Chain B: T.92, N.218 Ligand excluded by PLIP NAG.28: 3 residues within 4Å: Chain B: N.264, E.265, N.266 Ligand excluded by PLIP NAG.29: 2 residues within 4Å: Chain B: N.600, R.630 Ligand excluded by PLIP NAG.30: 2 residues within 4Å: Chain B: N.327, F.355 Ligand excluded by PLIP NAG.31: 4 residues within 4Å: Chain C: N.315, P.563, Q.564, L.566 Ligand excluded by PLIP NAG.32: 5 residues within 4Å: Chain C: Y.12, T.13, N.14, S.44, N.45 Ligand excluded by PLIP NAG.33: 4 residues within 4Å: Chain C: N.106, T.108, N.109, V.111 Ligand excluded by PLIP NAG.34: 3 residues within 4Å: Chain C: T.92, T.98, N.218 Ligand excluded by PLIP NAG.35: 3 residues within 4Å: Chain C: N.600, T.602, Q.628 Ligand excluded by PLIP NAG.36: 2 residues within 4Å: Chain C: Y.639, N.641 Ligand excluded by PLIP NAG.37: 3 residues within 4Å: Chain B: I.774, Y.776 Chain C: N.689 Ligand excluded by PLIP NAG.38: 2 residues within 4Å: Chain C: A.686, N.1054 Ligand excluded by PLIP NAG.39: 1 residues within 4Å: Chain C: N.327 Ligand excluded by PLIP NAG.40: 3 residues within 4Å: Chain C: N.264, E.265, N.266 Ligand excluded by PLIP NAG.41: 2 residues within 4Å: Chain C: N.587, T.588 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Liu, B. et al., An unconventional VH1-2 antibody tolerates escape mutations and shows an antigenic hotspot on SARS-CoV-2 spike. Cell Rep (2024)

Release Date

2024-05-15

Peptides

Spike glycoprotein: ABC
Light chain of D1F6 Fab: DFG
Heavy chain of D1F6 Fab: EHI

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

F
M

G
N

E
E

H
Q

I
R

Spike glycoprotein

Light chain of D1F6 Fab

Heavy chain of D1F6 Fab

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