SMTL ID : 7xod.1

SARS-CoV-2 Omicron BA.2 Variant Spike Trimer with three JMB2002 Fab Bound

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-3-mer

Ligands

2 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: T.713, N.714, L.919, Q.923, Q.1068 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.919 NAG-NAG.2: 2 residues within 4Å: Chain B: N.714, Q.1068 No protein-ligand interaction detected (PLIP)

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

NAG.3: 3 residues within 4Å: Chain A: E.1069, K.1070, N.1071 Ligand excluded by PLIP NAG.4: 3 residues within 4Å: Chain A: T.105, N.231, T.233 Ligand excluded by PLIP NAG.5: 3 residues within 4Å: Chain A: N.277, E.278, N.279 Ligand excluded by PLIP NAG.6: 3 residues within 4Å: Chain A: N.1095, G.1096, F.1100 Ligand excluded by PLIP NAG.7: 2 residues within 4Å: Chain A: N.798, S.800 Ligand excluded by PLIP NAG.8: 2 residues within 4Å: Chain A: N.706 Chain B: Y.793 Ligand excluded by PLIP NAG.9: 3 residues within 4Å: Chain A: Y.652, V.653, N.654 Ligand excluded by PLIP NAG.10: 2 residues within 4Å: Chain A: N.613, Q.641 Ligand excluded by PLIP NAG.11: 3 residues within 4Å: Chain A: E.306, N.600, T.601 Ligand excluded by PLIP NAG.12: 2 residues within 4Å: Chain A: N.328, Q.577 Ligand excluded by PLIP NAG.13: 1 residues within 4Å: Chain A: N.162 Ligand excluded by PLIP NAG.14: 3 residues within 4Å: Chain B: A.703, E.1069, N.1071 Ligand excluded by PLIP NAG.15: 3 residues within 4Å: Chain B: T.105, N.231, T.233 Ligand excluded by PLIP NAG.16: 2 residues within 4Å: Chain B: E.278, N.279 Ligand excluded by PLIP NAG.17: 2 residues within 4Å: Chain B: N.1095, F.1100 Ligand excluded by PLIP NAG.18: 2 residues within 4Å: Chain B: N.798, S.800 Ligand excluded by PLIP NAG.19: 2 residues within 4Å: Chain B: N.706 Chain C: Y.793 Ligand excluded by PLIP NAG.20: 3 residues within 4Å: Chain B: E.651, Y.652, N.654 Ligand excluded by PLIP NAG.21: 1 residues within 4Å: Chain B: N.613 Ligand excluded by PLIP NAG.22: 2 residues within 4Å: Chain B: N.600, T.601 Ligand excluded by PLIP NAG.23: 3 residues within 4Å: Chain B: N.328, Q.577, L.579 Ligand excluded by PLIP NAG.24: 4 residues within 4Å: Chain B: S.109, N.162, C.163, T.164 Ligand excluded by PLIP NAG.25: 1 residues within 4Å: Chain B: N.1131 Ligand excluded by PLIP NAG.26: 1 residues within 4Å: Chain C: N.654 Ligand excluded by PLIP NAG.27: 2 residues within 4Å: Chain C: N.328, Q.577 Ligand excluded by PLIP NAG.28: 3 residues within 4Å: Chain C: T.105, N.231, T.233 Ligand excluded by PLIP NAG.29: 1 residues within 4Å: Chain C: N.600 Ligand excluded by PLIP NAG.30: 3 residues within 4Å: Chain C: E.1069, K.1070, N.1071 Ligand excluded by PLIP NAG.31: 3 residues within 4Å: Chain C: I.1129, V.1130, N.1131 Ligand excluded by PLIP NAG.32: 2 residues within 4Å: Chain C: N.1095, T.1097 Ligand excluded by PLIP NAG.33: 2 residues within 4Å: Chain C: S.109, N.162 Ligand excluded by PLIP NAG.34: 3 residues within 4Å: Chain C: N.613, C.614, Q.641 Ligand excluded by PLIP NAG.35: 1 residues within 4Å: Chain C: N.706 Ligand excluded by PLIP NAG.36: 3 residues within 4Å: Chain C: N.798, S.800, Q.801 Ligand excluded by PLIP NAG.37: 1 residues within 4Å: Chain C: N.279 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Xu, Y. et al., Structural and biochemical mechanism for increased infectivity and immune evasion of Omicron BA.2 variant compared to BA.1 and their possible mouse origins. Cell Res. (2022)

Release Date

2022-06-15

Peptides

Spike glycoprotein: ABC
Heavy chain of JMB2002 Fab: DGJ
Light chain of JMB2002 Fab: EHK
Nanobody: FIL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
X

G
U

J
R

E
Y

H
V

K
S

F
Z

I
W

L
T

Spike glycoprotein

Heavy chain of JMB2002 Fab

Light chain of JMB2002 Fab

Nanobody

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