SMTL ID : 8zc0.1

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

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-mer

Ligands

18 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: S.688, N.689 Chain C: Y.776 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 3 residues within 4Å: Chain A: N.697, L.902, Q.906 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 2 residues within 4Å: Chain A: N.781, Q.784 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 4 residues within 4Å: Chain A: N.1078, T.1080, H.1081, F.1083 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 1 residues within 4Å: Chain A: N.1114 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 2 residues within 4Å: Chain A: N.315, Q.564 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: 2 residues within 4Å: Chain B: I.1112, N.1114 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 2 residues within 4Å: Chain B: N.106, V.155 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:V.155 NAG-NAG.10: 3 residues within 4Å: Chain B: N.315, P.563, Q.564 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 2 residues within 4Å: Chain B: N.697, L.902 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 3 residues within 4Å: Chain B: N.781, S.783, Q.784 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 3 residues within 4Å: Chain B: N.1078, T.1080, F.1083 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 2 residues within 4Å: Chain C: N.600, T.602 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 3 residues within 4Å: Chain C: N.697, L.902, Q.906 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 1 residues within 4Å: Chain C: N.781 No protein-ligand interaction detected (PLIP) NAG-NAG.17: 4 residues within 4Å: Chain C: N.1078, G.1079, H.1081, F.1083 No protein-ligand interaction detected (PLIP) NAG-NAG.18: 1 residues within 4Å: Chain C: N.1114 No protein-ligand interaction detected (PLIP)

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

NAG.19: 3 residues within 4Å: Chain A: Y.12, N.14, N.45 Ligand excluded by PLIP NAG.20: 4 residues within 4Å: Chain A: N.106, T.108, N.109, V.111 Ligand excluded by PLIP NAG.21: 3 residues within 4Å: Chain A: N.264, N.266 Chain B: K.542 Ligand excluded by PLIP NAG.22: 4 residues within 4Å: Chain A: N.600, T.602, Q.628, R.630 Ligand excluded by PLIP NAG.23: 2 residues within 4Å: Chain A: N.1054 Chain C: Q.875 Ligand excluded by PLIP NAG.24: 2 residues within 4Å: Chain A: Y.639, N.641 Ligand excluded by PLIP NAG.25: 3 residues within 4Å: Chain B: Y.12, N.14, N.45 Ligand excluded by PLIP NAG.26: 2 residues within 4Å: Chain B: T.92, N.218 Ligand excluded by PLIP NAG.27: 2 residues within 4Å: Chain B: N.266 Chain C: K.542 Ligand excluded by PLIP NAG.28: 3 residues within 4Å: Chain B: N.327, N.354, F.355 Ligand excluded by PLIP NAG.29: 2 residues within 4Å: Chain B: N.600, Q.628 Ligand excluded by PLIP NAG.30: 2 residues within 4Å: Chain B: A.686, N.1054 Ligand excluded by PLIP NAG.31: 2 residues within 4Å: Chain B: Y.639, N.641 Ligand excluded by PLIP NAG.32: 3 residues within 4Å: Chain C: N.106, T.108, V.111 Ligand excluded by PLIP NAG.33: 2 residues within 4Å: Chain C: N.264, N.266 Ligand excluded by PLIP NAG.34: 2 residues within 4Å: Chain C: N.315, Q.564 Ligand excluded by PLIP NAG.35: 1 residues within 4Å: Chain C: N.327 Ligand excluded by PLIP NAG.36: 3 residues within 4Å: Chain B: I.774, Y.776 Chain C: N.689 Ligand excluded by PLIP NAG.37: 2 residues within 4Å: Chain C: A.686, N.1054 Ligand excluded by PLIP NAG.38: 3 residues within 4Å: Chain C: N.14, F.43, N.45 Ligand excluded by PLIP NAG.39: 2 residues within 4Å: Chain C: I.217, N.218 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
G

F
M

G
N

E
H

H
Q

I
R

Spike glycoprotein

Light chain of D1F6 Fab

Heavy chain of D1F6 Fab

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