SMTL ID : 8zc2.1

SARS-CoV-2 Omicron BA.2 spike trimer (6P) in complex with D1F6 Fab, head-to-head aggregate

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-6-6-6-mer

Ligands

7 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: 5 residues within 4Å: Chain A: N.106, T.108, N.109, V.111, V.155 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:V.155 NAG-NAG.2: 3 residues within 4Å: Chain A: N.781, S.783, Q.784 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.784 NAG-NAG.3: 3 residues within 4Å: Chain A: I.1112, V.1113, N.1114 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 3 residues within 4Å: Chain B: N.106, T.108, V.155 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:V.155 NAG-NAG.5: 3 residues within 4Å: Chain B: N.1078, T.1080, F.1083 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 3 residues within 4Å: Chain B: N.315, Q.564, T.565 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:T.565 NAG-NAG.7: 4 residues within 4Å: Chain C: N.1078, G.1079, H.1081, F.1083 No protein-ligand interaction detected (PLIP)

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

NAG.8: 3 residues within 4Å: Chain A: Y.12, N.14, N.45 Ligand excluded by PLIP NAG.9: 1 residues within 4Å: Chain A: N.266 Ligand excluded by PLIP NAG.10: 3 residues within 4Å: Chain A: N.600, T.602, Q.628 Ligand excluded by PLIP NAG.11: 3 residues within 4Å: Chain A: S.688, N.689 Chain C: Y.776 Ligand excluded by PLIP NAG.12: 4 residues within 4Å: Chain A: N.697, T.699, L.902, Q.906 Ligand excluded by PLIP NAG.13: 4 residues within 4Å: Chain A: N.1078, T.1080, H.1081, F.1083 Ligand excluded by PLIP NAG.14: 2 residues within 4Å: Chain A: N.315, Q.564 Ligand excluded by PLIP NAG.15: 3 residues within 4Å: Chain B: Y.12, N.14, N.45 Ligand excluded by PLIP NAG.16: 2 residues within 4Å: Chain B: T.92, N.218 Ligand excluded by PLIP NAG.17: 2 residues within 4Å: Chain B: N.266 Chain C: K.542 Ligand excluded by PLIP NAG.18: 2 residues within 4Å: Chain B: N.600, Q.628 Ligand excluded by PLIP NAG.19: 5 residues within 4Å: Chain A: I.774, Y.776 Chain B: Y.687, S.688, N.689 Ligand excluded by PLIP NAG.20: 2 residues within 4Å: Chain A: Q.875 Chain B: N.1054 Ligand excluded by PLIP NAG.21: 2 residues within 4Å: Chain B: N.697, L.902 Ligand excluded by PLIP NAG.22: 3 residues within 4Å: Chain B: N.781, S.783, Q.784 Ligand excluded by PLIP NAG.23: 3 residues within 4Å: Chain B: F.326, N.327, F.355 Ligand excluded by PLIP NAG.24: 4 residues within 4Å: Chain C: N.106, T.108, V.111, F.141 Ligand excluded by PLIP NAG.25: 2 residues within 4Å: Chain C: N.600, T.602 Ligand excluded by PLIP NAG.26: 6 residues within 4Å: Chain B: Q.875 Chain C: A.686, A.693, E.1052, K.1053, N.1054 Ligand excluded by PLIP NAG.27: 4 residues within 4Å: Chain C: N.697, L.902, Q.906, Q.1051 Ligand excluded by PLIP NAG.28: 1 residues within 4Å: Chain C: N.781 Ligand excluded by PLIP NAG.29: 1 residues within 4Å: Chain C: N.1114 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

2024-05-29

Peptides

Spike glycoprotein: ABCJKL
Light chain of D1F6 Fab: DFGMOP
Heavy chain of D1F6 Fab: EHINQR

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

J
D

K
E

L
F

D
G

F
M

G
N

M
I

O
K

P
L

E
H

H
Q

I
R

N
J

Q
O

R
P

Spike glycoprotein

Light chain of D1F6 Fab

Heavy chain of D1F6 Fab

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