SMTL ID : 8zc6.1

SARS-CoV-2 Omicron BA.4 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

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

NAG.1: 4 residues within 4Å: Chain A: N.104, T.106, N.107, V.109 Ligand excluded by PLIP NAG.2: 2 residues within 4Å: Chain A: E.263, N.264 Ligand excluded by PLIP NAG.3: 3 residues within 4Å: Chain A: N.598, T.600, Q.626 Ligand excluded by PLIP NAG.4: 4 residues within 4Å: Chain A: S.686, N.687 Chain C: I.772, Y.774 Ligand excluded by PLIP NAG.5: 4 residues within 4Å: Chain A: N.695, T.697, L.900, Q.904 Ligand excluded by PLIP NAG.6: 4 residues within 4Å: Chain A: K.773, N.779, F.780, S.781 Ligand excluded by PLIP NAG.7: 4 residues within 4Å: Chain A: N.1076, T.1078, H.1079, F.1081 Ligand excluded by PLIP NAG.8: 4 residues within 4Å: Chain A: P.312, N.313, P.561, Q.562 Ligand excluded by PLIP NAG.9: 4 residues within 4Å: Chain A: Y.12, T.13, N.14, N.45 Ligand excluded by PLIP NAG.10: 3 residues within 4Å: Chain B: Y.12, N.14, N.45 Ligand excluded by PLIP NAG.11: 2 residues within 4Å: Chain B: N.598, Q.626 Ligand excluded by PLIP NAG.12: 4 residues within 4Å: Chain B: N.104, T.106, N.107, V.109 Ligand excluded by PLIP NAG.13: 3 residues within 4Å: Chain B: N.313, P.561, Q.562 Ligand excluded by PLIP NAG.14: 4 residues within 4Å: Chain B: T.694, N.695, L.900, F.1087 Ligand excluded by PLIP NAG.15: 4 residues within 4Å: Chain B: K.773, N.779, F.780, S.781 Ligand excluded by PLIP NAG.16: 3 residues within 4Å: Chain B: N.1076, T.1078, F.1081 Ligand excluded by PLIP NAG.17: 2 residues within 4Å: Chain C: N.687, N.688 Ligand excluded by PLIP NAG.18: 5 residues within 4Å: Chain C: T.694, N.695, L.900, Q.1049, F.1087 Ligand excluded by PLIP NAG.19: 5 residues within 4Å: Chain C: K.773, F.778, N.779, F.780, S.781 Ligand excluded by PLIP NAG.20: 4 residues within 4Å: Chain C: N.1076, G.1077, H.1079, F.1081 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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