SMTL ID : 7wjz.1

Omicron Spike bitrimer with 6m6 antibody

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-6-6-6-mer

Ligands

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

NAG.1: 4 residues within 4Å: Chain A: N.120, A.121, T.122, V.125 Ligand excluded by PLIP NAG.2: 3 residues within 4Å: Chain A: N.277, E.278, N.279 Ligand excluded by PLIP NAG.3: 2 residues within 4Å: Chain A: N.328, Q.577 Ligand excluded by PLIP NAG.4: 7 residues within 4Å: Chain A: F.335, D.336, F.339, N.340, V.364, N.367, L.368 Ligand excluded by PLIP NAG.5: 2 residues within 4Å: Chain A: N.706 Chain G: Y.793 Ligand excluded by PLIP NAG.6: 3 residues within 4Å: Chain A: N.714, Q.923, Q.1068 Ligand excluded by PLIP NAG.7: 2 residues within 4Å: Chain A: N.798, S.800 Ligand excluded by PLIP NAG.8: 5 residues within 4Å: Chain D: N.120, A.121, T.122, N.123, V.125 Ligand excluded by PLIP NAG.9: 3 residues within 4Å: Chain D: N.277, E.278, N.279 Ligand excluded by PLIP NAG.10: 2 residues within 4Å: Chain D: N.328, Q.577 Ligand excluded by PLIP NAG.11: 7 residues within 4Å: Chain D: F.335, D.336, F.339, N.340, V.364, N.367, L.368 Ligand excluded by PLIP NAG.12: 2 residues within 4Å: Chain A: Y.793 Chain D: N.706 Ligand excluded by PLIP NAG.13: 3 residues within 4Å: Chain D: N.714, Q.923, Q.1068 Ligand excluded by PLIP NAG.14: 2 residues within 4Å: Chain D: N.798, S.800 Ligand excluded by PLIP NAG.15: 1 residues within 4Å: Chain D: N.1131 Ligand excluded by PLIP NAG.16: 4 residues within 4Å: Chain G: N.277, E.278, N.279, T.281 Ligand excluded by PLIP NAG.17: 3 residues within 4Å: Chain G: N.328, P.576, Q.577 Ligand excluded by PLIP NAG.18: 7 residues within 4Å: Chain G: F.335, D.336, F.339, N.340, V.364, N.367, L.368 Ligand excluded by PLIP NAG.19: 2 residues within 4Å: Chain G: N.706, N.707 Ligand excluded by PLIP NAG.20: 4 residues within 4Å: Chain G: N.714, L.919, Q.923, Q.1068 Ligand excluded by PLIP NAG.21: 3 residues within 4Å: Chain G: N.798, S.800, Q.801 Ligand excluded by PLIP NAG.22: 4 residues within 4Å: Chain G: A.703, E.1069, K.1070, N.1071 Ligand excluded by PLIP NAG.23: 1 residues within 4Å: Chain G: N.1131 Ligand excluded by PLIP NAG.24: 5 residues within 4Å: Chain J: Y.28, T.29, N.30, S.60, N.61 Ligand excluded by PLIP NAG.25: 2 residues within 4Å: Chain J: N.277, N.279 Ligand excluded by PLIP NAG.26: 3 residues within 4Å: Chain J: N.328, P.576, Q.577 Ligand excluded by PLIP NAG.27: 7 residues within 4Å: Chain J: F.335, D.336, F.339, N.340, V.364, N.367, L.368 Ligand excluded by PLIP NAG.28: 3 residues within 4Å: Chain J: N.714, Q.923, Q.1068 Ligand excluded by PLIP NAG.29: 2 residues within 4Å: Chain J: N.798, S.800 Ligand excluded by PLIP NAG.30: 1 residues within 4Å: Chain J: N.1131 Ligand excluded by PLIP NAG.31: 5 residues within 4Å: Chain M: Y.28, T.29, N.30, S.60, N.61 Ligand excluded by PLIP NAG.32: 4 residues within 4Å: Chain M: N.120, A.121, T.122, N.123 Ligand excluded by PLIP NAG.33: 2 residues within 4Å: Chain M: N.277, N.279 Ligand excluded by PLIP NAG.34: 2 residues within 4Å: Chain M: N.328, Q.577 Ligand excluded by PLIP NAG.35: 6 residues within 4Å: Chain M: D.336, F.339, N.340, V.364, N.367, L.368 Ligand excluded by PLIP NAG.36: 2 residues within 4Å: Chain M: N.706, N.707 Ligand excluded by PLIP NAG.37: 3 residues within 4Å: Chain M: T.713, N.714, Q.1068 Ligand excluded by PLIP NAG.38: 2 residues within 4Å: Chain M: N.798, S.800 Ligand excluded by PLIP NAG.39: 1 residues within 4Å: Chain M: N.1131 Ligand excluded by PLIP NAG.40: 5 residues within 4Å: Chain P: Y.28, T.29, N.30, S.60, N.61 Ligand excluded by PLIP NAG.41: 4 residues within 4Å: Chain P: N.120, A.121, T.122, N.123 Ligand excluded by PLIP NAG.42: 2 residues within 4Å: Chain P: N.277, N.279 Ligand excluded by PLIP NAG.43: 2 residues within 4Å: Chain P: N.328, Q.577 Ligand excluded by PLIP NAG.44: 6 residues within 4Å: Chain P: D.336, F.339, N.340, V.364, N.367, L.368 Ligand excluded by PLIP NAG.45: 2 residues within 4Å: Chain P: N.613, T.615 Ligand excluded by PLIP NAG.46: 3 residues within 4Å: Chain M: Y.793 Chain P: N.706, N.707 Ligand excluded by PLIP NAG.47: 5 residues within 4Å: Chain P: T.713, N.714, L.919, Q.923, Q.1068 Ligand excluded by PLIP NAG.48: 2 residues within 4Å: Chain P: N.798, S.800 Ligand excluded by PLIP NAG.49: 1 residues within 4Å: Chain P: N.1131 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, Y. et al., A broadly neutralizing antibody against SARS-CoV-2 Omicron variant infection exhibiting a novel trimer dimer conformation in spike protein binding. Cell Res. (2022)

Release Date

2022-07-13

Peptides

Spike glycoprotein: ADGJMP
6m6 heavy chain: BEHKNQ
6m6 light chain: CFILOR

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

D
I

G
J

J
K

M
L

P
M

B
A

E
D

H
E

K
F

N
G

Q
H

C
C

F
N

I
O

L
P

O
Q

R
R

Spike glycoprotein

6m6 heavy chain

6m6 light chain

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